Single-cell RNA Report

SampleSid SijbrandijCancer typeOsteosarcoma

About this report

An interactive summary of the single-cell RNA-seq neoantigen pipeline for this sample. Each section below covers one stage: who is in the tumor, whether the T cells are engaged, which mutations are actually transcribed in tumor cells, how uniform the tumor is, and the resulting ranked vaccine-target shortlist. Use the nav bar or the cards below.

Neoantigen RNA allele frequency

Single-cell vs bulk RNA allele frequency for each candidate neoantigen and genomic site.

Tumor heterogeneity & subclones

Subclone structure, heterogeneity score, clonal-vs-subclonal neoantigens, and HLA-loss screen.

Subclonal Analysis

Subclone populations and a neoantigen-presence-by-subclone matrix (RNA-expressed).

Neoantigen prioritization

The Tier1 vaccine-target shortlist and the full ranked, tiered candidate table.

Neoantigen RNA allele frequency

Candidate neoantigens shown with their single-cell RNA allele frequency next to the bulk RNA numbers — both per mutation and aggregated per genomic site.

Per-neoantigen single-cell vs bulk allele frequency

Every candidate neoantigen (mutation) with its single-cell RNA allele frequency alongside the bulk numbers. HLA-locus mutations are excluded.

Gene	Mutation	Bulk RNA-AF	Bulk RNA expr	sc RNA-AF (all cells)	sc depth (DP)	Cells covered	Cells w/ mutant	sc RNA-AF (malignant)	Malignant depth
RPS19	RPS19:p.Val30Ala	0.01	276.61	0.00	28,198	3,966	7	0.00	129
NDUFA11	NDUFA11:p.Arg104Cys	0.08	103.46	0.00	3,744	1,858	4	0.00	24
EZR	EZR:p.Pro2Ser		87.28	0.00	1,937	1,317	3	0.02	58
PEPD	PEPD:p.Gly50Ser		11.59	0.00	999	761	0	0.00	8
POLR2I	POLR2I:p.Ala48Val		8.57	0.00	877	706	0	0.00	11
CCNQ	CCNQ:p.Gly81Asp	0.04	6.91	0.00	661	567	1	0.00	1
EXOC4	EXOC4:p.Ser34Ile	0.20	159.69	0.13	588	503	72	0.29	52
MCRIP2	MCRIP2:p.Glu30Lys		6.48	0.00	519	432	0	0.00	7
PCBP1	PCBP1:p.Arg306His	0.00	209.16	0.00	516	456	0	0.00	2
MCMBP	MCMBP:p.Gly17Glu		37.69	0.00	418	387	0	0.00	13
SLC25A43	SLC25A43:p.Ser83Arg		13.11	0.00	382	342	0	0.00	18
FAM168B	FAM168B:p.Ala31Val		37.28	0.00	363	328	0	0.00	7
ITGB1	ITGB1:p.Gly550Asp	0.00	2266.71	0.00	332	260	0	0.00	26
VSIG4	VSIG4:p.Ile203Val		83.23	0.00	249	204	0		0
TMEM44	TMEM44:p.Leu50Arg		18.21	0.00	238	207	1	0.00	16
TBC1D22A	TBC1D22A:p.Ala98Thr		24.24	0.00	234	226	0	0.00	6
TGFB1	TGFB1:p.Arg372His		159.03	0.00	184	177	0	0.00	7
TMBIM4	TMBIM4:p.Arg230Gln		87.47	0.00	179	171	0	0.00	8
C6orf62	C6orf62:p.Pro57Ser		161.31	0.00	170	163	0	0.00	9
WLS	WLS:p.Trp460Arg		119.27	0.00	159	137	0	0.00	4
NOL4L	NOL4L:p.Arg270Trp		15.46	0.00	157	137	0	0.00	2
VSTM4	VSTM4:p.Ala94Thr		6.17	0.00	156	133	0	0.00	12
RASIP1	RASIP1:p.Ala78Val		1.78	0.00	134	97	0	0.00	1
LAMA4	LAMA4:p.Gly1688Asp	0.00	625.54	0.00	124	111	0	0.00	11
TMEM131L	TMEM131L:p.Ala16Thr		15.85	0.00	116	112	0	0.00	7
DYNC1H1	DYNC1H1:p.Val314Ile	0.43	390.57	0.29	116	112	34	0.44	9
PHF3	PHF3:p.Arg971Trp		211.67	0.00	115	113	0	0.00	4
FGL2	FGL2:p.Asp212Tyr	0.00	101.65	0.00	115	105	0		0
JUP	JUP:p.Ala617Val		50.10	0.01	111	92	1	0.00	3
COASY	COASY:p.Gly44Asp		17.65	0.00	106	101	0	0.00	1
SF3A2	SF3A2:p.Gly399Glu		61.62	0.00	106	103	0	0.00	7
TRMO	TRMO:p.Gly205Glu	0.06	79.34	0.06	102	96	6	0.00	1
FUCA1	FUCA1:p.Arg178Cys		29.40	0.00	98	84	0		0
FXR1	FXR1:p.Gly298Arg		347.50	0.01	95	91	1	0.00	2
IL17RC	IL17RC:p.Ala587Val		7.83	0.00	81	78	0	0.00	1
MAGEB1	MAGEB1:p.Ala290Val	0.01	12.03	0.00	80	68	0	0.00	3
UBXN4	UBXN4:p.Lys480Met		101.89	0.00	78	76	0	0.00	2
ETV2	ETV2:p.Gly264Asp		0.90	0.00	77	74	0		0
CTTNBP2NL	CTTNBP2NL:p.Arg96His	0.01	30.79	0.00	75	72	0	0.00	1
LRBA	LRBA:p.Ala49Val	0.00	69.91	0.00	75	73	0	0.00	4
XRN2	XRN2:p.Gly375Trp	0.01	95.52	0.00	73	72	0	0.00	5
HIP1	HIP1:p.Gly956Asp	0.00	43.31	0.00	69	65	0	0.00	3
OTUD6B	OTUD6B:p.Thr6Ser		31.18	0.00	69	65	0	0.00	4
FHL3	FHL3:p.Pro143Ser	0.02	22.22	0.00	66	63	0		0
UBE3A	UBE3A:p.Asp698Asn		150.35	0.00	66	65	0	0.00	2
SPPL2A	SPPL2A:p.Gly282Asp	0.00	177.06	0.00	65	63	0	0.00	3
URI1	URI1:p.Asp153Asn		91.89	0.03	63	61	2		0
ATP1A1	ATP1A1:p.Glu544Lys		91.10	0.00	62	61	0		0
SYDE2	SYDE2:p.Gly141Val		118.31	0.00	61	58	0	0.00	13
IGBP1	IGBP1:p.Ile203Thr		41.84	0.00	61	60	0	0.00	1
NGDN	NGDN:p.Ala280Thr		41.72	0.00	59	58	0	0.00	3
FASN	FASN:p.Gly8Asp		28.55	0.00	58	55	0	0.00	2
SPATS2L	SPATS2L:p.Ala450Thr		79.31	0.00	55	55	0	0.00	1
STX8	STX8:p.Pro234Ser	0.03	66.98	0.00	52	51	0		0
CYLD	CYLD:p.Gly596Asp		49.83	0.00	51	49	0	0.00	1
RIF1	RIF1:p.Val1366Ile		60.65	0.00	50	50	0	0.00	2
ABCF2	ABCF2:p.Asp421Glu	0.02	8.82	0.00	50	46	0	0.00	3
ABCB7	ABCB7:p.Gly388Ser		72.79	0.00	50	47	0		0
SEC24D	SEC24D:p.Ala284Val	0.00	109.50	0.00	49	44	0	0.00	3
SLC25A39	SLC25A39:p.Arg186Trp		12.46	0.00	47	45	0	0.00	1
PLSCR3	PLSCR3:p.Gly287Ser		7.98	0.00	45	45	0	0.00	1
GNPTAB	GNPTAB:p.Ala1122Ser	0.01	82.06	0.00	43	39	0		0
PRRC2C	PRRC2C:p.Thr2152Ile		365.42	0.00	41	41	0	0.00	4
MRPS5	MRPS5:p.Ser386Phe		52.53	0.00	41	40	0	0.00	2
PRRC2C	PRRC2C:p.Ala2147Val		365.42	0.00	39	39	0	0.00	4
RIOK1	RIOK1:p.Glu250Lys		117.44	0.00	39	39	0		0
SIRPA	SIRPA:p.Ala454Val	0.10	22.94	0.00	38	37	0		0
TMEM131	TMEM131:p.Ser224Asn		82.03	0.00	37	36	0	0.00	3
LRRFIP2	LRRFIP2:p.Arg345Gln		395.19	0.00	36	35	0		0
ADGRF5	ADGRF5:p.Asn1279Ser		30.56	0.00	36	33	0		0
SPACA6	SPACA6:p.Ser279Arg		2.35	0.00	36	34	0	0.00	3
LENG8	LENG8:p.Ala213Thr	0.01	73.79	0.00	35	35	0	0.00	1
KDM3B	KDM3B:p.Pro633Ser	0.22	97.25	0.00	34	34	0	0.00	1
ATP9B	ATP9B:p.Arg407His		69.21	0.00	32	32	0	0.00	2
HLTF	HLTF:p.Pro239Leu	0.00	35.63	0.00	30	30	0	0.00	1
BCL7A	BCL7A:p.Asp88Asn		4.58	0.00	28	27	0	0.00	4
MCU	MCU:p.Leu9Val		64.73	0.00	27	27	0	0.00	2
PARP4	PARP4:p.Ala373Thr		36.47	0.00	27	27	0	0.00	3
SNRNP40	SNRNP40:p.Arg260Ser		27.52	0.00	26	26	0	0.00	1
SLC25A12	SLC25A12:p.Ile347Thr	0.37	59.50	0.35	26	25	9		0
CHD9	CHD9:p.Arg1481Trp	0.01	263.75	0.00	26	23	0		0
NR2F2	NR2F2:p.Gly65Val		36.17	0.00	25	24	0		0
TRIM6	TRIM6:p.Ala103Thr		15.09	0.00	24	23	0		0
KRT18	KRT18:p.Ala287Ser	0.12	6.04	0.00	24	24	0		0
CDC25B	CDC25B:p.Lys192Thr		18.17	0.00	24	23	0		0
UBR4	UBR4:p.Ala4907Val		65.82	0.00	23	23	0	0.00	1
RIPK2	RIPK2:p.Asp211Asn		36.79	0.00	23	22	0		0
MAP4K1	MAP4K1:p.Gly517Arg		4.16	0.00	23	23	0	0.00	1
PRKD2	PRKD2:p.Arg192His		13.89	0.00	23	22	0		0
XPO5	XPO5:p.Lys704Thr		33.56	0.00	22	20	0	0.00	2
SCRIB	SCRIB:p.Ala1461Thr		6.09	0.00	22	22	0		0
ARHGAP1	ARHGAP1:p.Ala285Thr		23.32	0.00	22	22	0		0
TNS2	TNS2:p.Ala484Val		137.79	0.00	22	21	0	0.00	2
LTBP2	LTBP2:p.Gly1088Asp		32.88	0.00	21	21	0	0.00	3
RNF40	RNF40:p.Gly436Glu		42.72	0.00	21	21	0	0.00	1
ARHGAP28	ARHGAP28:p.Ala235Val		29.45	0.05	21	20	1	0.00	4
ANKZF1	ANKZF1:p.Ala650Val		30.96	0.00	20	20	0	0.00	2
PHRF1	PHRF1:p.Pro221Ser	0.00	21.47	0.00	20	19	0	0.00	3
BACE1	BACE1:p.Arg408Trp		44.90	0.00	20	20	0	0.00	1
WWC3	WWC3:p.Tyr240Asn		25.59	0.00	19	18	0	0.00	3
VPS37C	VPS37C:p.Pro267Ser	0.18	4.34	0.00	18	18	0	0.00	1
CARS2	CARS2:p.Ala235Thr		20.00	0.00	18	18	0		0
CSTF1	CSTF1:p.Ala142Thr		36.85	0.00	18	18	0		0
NCOA1	NCOA1:p.Ala310Val		68.94	0.00	17	17	0	0.00	1
MSL2	MSL2:p.Ala514Val	0.01	89.92	0.00	17	17	0	0.00	1
RBM28	RBM28:p.Ala464Thr		153.49	0.00	17	17	0	0.00	3
NEO1	NEO1:p.Met855Ile	0.00	186.04	0.00	17	17	0	0.00	2
HDAC5	HDAC5:p.Arg266Cys		57.69	0.00	17	17	0	0.00	1
WDR44	WDR44:p.Ala204Val	0.01	20.90	0.00	17	17	0	0.00	1
HPS1	HPS1:p.Phe301Val		13.15	0.00	16	16	0		0
ULK2	ULK2:p.Val22Leu		12.25	0.00	16	16	0		0
ZNF880	ZNF880:p.Cys413Phe	0.37	33.74	0.31	16	15	5	0.33	3
UBR4	UBR4:p.Arg1628Gln		65.82	0.00	15	15	0		0
CDC40	CDC40:p.Val507Ile		55.37	0.00	15	15	0		0
BRAP	BRAP:p.Arg534His	0.01	23.43	0.00	15	15	0		0
SLC43A2	SLC43A2:p.Val380Ile		10.28	0.00	15	15	0		0
KIF1C	KIF1C:p.Glu456Lys	0.42	84.68	0.00	15	14	0		0
SLC33A1	SLC33A1:p.Ala131Val	0.01	36.83	0.00	14	14	0	0.00	1
TGS1	TGS1:p.Ala709Val		25.10	0.00	14	14	0	0.00	1
ZNF606	ZNF606:p.Gly305Ser		25.69	0.00	14	14	0		0
BTD	BTD:p.Phe423Val	0.27	11.63	0.08	13	13	1		0
LNP1	LNP1:p.His65Leu	0.09	7.03	0.15	13	12	2		0
BLTP3B	BLTP3B:p.Ala473Val		62.80	0.00	13	13	0	0.00	1
NACC1	NACC1:p.Thr373Ile		16.16	0.00	13	13	0		0
LIN7B	LIN7B:p.Pro175Leu		2.57	0.00	13	13	0	0.00	1
NKRF	NKRF:p.Val221Ile	0.01	18.96	0.00	13	13	0	0.00	1
TARS2	TARS2:p.Ala439Thr		24.13	0.00	12	12	0	0.00	1
NUP210	NUP210:p.Ala1857Thr		1.28	0.00	12	12	0		0
ZC3H12C	ZC3H12C:p.Glu434Lys		47.33	0.00	12	12	0		0
EHD3	EHD3:p.Asn295His		25.58	0.00	11	10	0		0
ADAMTS2	ADAMTS2:p.Asp650Asn		7.10	0.00	11	11	0	0.00	1
ANLN	ANLN:p.Ser553Cys	0.00	117.94	0.00	11	11	0		0
VWF	VWF:p.Glu954Gly		164.23	0.00	11	10	0		0
TGFBR3	TGFBR3:p.Cys572Tyr		11.15	0.00	10	10	0		0
CYP1B1	CYP1B1:p.Arg43Trp		4.67	0.00	10	9	0		0
TNIK	TNIK:p.Arg299His	0.00	190.33	0.00	10	10	0	0.00	2
HERC3	HERC3:p.Glu382Lys		161.27	0.00	10	10	0	0.00	1
SCAF8	SCAF8:p.Pro694Ser	0.02	108.04	0.00	10	10	0		0
HSH2D	HSH2D:p.Ala316Ser		0.07	0.00	9	9	0		0
ZNF436	ZNF436:p.Ser207Cys	0.47	13.06	0.38	8	8	3	1.00	2
LYST	LYST:p.Gly1812Asp		36.63	0.00	8	8	0		0
NUP188	NUP188:p.Ala1087Thr		49.67	0.00	8	8	0	0.00	1
ABCC4	ABCC4:p.Ala859Val		47.08	0.00	8	8	0	0.00	2
EEF2KMT	EEF2KMT:p.Ala231Thr		3.29	0.00	8	8	0		0
CES3	CES3:p.Ala90Val		0.76	0.00	8	8	0	0.00	1
ROBO2	ROBO2:p.Asn1068Lys	0.07	53.45	0.86	7	7	6		0
IFT122	IFT122:p.Arg798His	0.01	24.46	0.00	7	7	0		0
VPS13B	VPS13B:p.Ser3731Phe	0.05	118.45	0.00	7	7	0		0
MYO9A	MYO9A:p.Asp523Val	0.01	123.09	0.00	7	7	0		0
PAK4	PAK4:p.Gly477Asp		5.23	0.00	7	7	0	0.00	1
BAIAP2L2	BAIAP2L2:p.Gly506Asp		0.44	0.00	7	7	0	0.00	2
AHDC1	AHDC1:p.Arg832His		5.70	0.00	6	6	0		0
CUL9	CUL9:p.Asp394Tyr	0.06	29.14	0.00	6	6	0		0
ZFYVE1	ZFYVE1:p.Ala503Val		16.02	0.00	6	6	0		0
EPG5	EPG5:p.Ala869Thr	0.09	41.72	0.00	6	6	0		0
CTDP1	CTDP1:p.Gly476Cys	0.50	7.88	0.00	6	6	0		0
SMARCAL1	SMARCAL1:p.Gly463Arg		6.21	0.00	5	5	0		0
CD200R1	CD200R1:p.Pro258Leu		8.02	0.00	5	5	0		0
TANC2	TANC2:p.Arg1015Trp		157.83	0.00	5	5	0		0
BICRA	BICRA:p.Arg1392Cys		2.23	0.00	5	5	0		0
MORN1	MORN1:p.Cys196Tyr		2.21	0.00	4	4	0	0.00	1
PGAP1	PGAP1:p.Thr691Met		22.91	0.00	4	4	0		0
OPLAH	OPLAH:p.Pro841Ser		13.54	0.00	4	4	0		0
CLDN10	CLDN10:p.Ala47Thr		0.93	0.00	4	1	0		0
TTBK2	TTBK2:p.Pro593Arg		30.90	0.00	4	4	0		0
MED16	MED16:p.Val318Met		22.70	0.00	4	4	0		0
C19orf44	C19orf44:p.Ala649Val		6.75	0.00	4	4	0	0.00	2
MAP3K10	MAP3K10:p.Arg649Trp		3.68	0.00	4	4	0		0
PLA2R1	PLA2R1:p.Trp519Leu	0.01	17.79	0.00	3	3	0	0.00	1
CRACD	CRACD:p.Ala647Val		24.21	0.00	3	3	0	0.00	1
SYNE1	SYNE1:p.Ala4264Val		252.51	0.00	3	3	0		0
RAB11FIP3	RAB11FIP3:p.Ala101Val		14.12	0.00	3	3	0		0
ADGRG5	ADGRG5:p.Ala318Val		0.08	0.00	3	3	0		0
CD300H	CD300H:p.Ser157Asn		0.00	0.00	3	3	0		0
PHF6	PHF6:p.Arg347Gln		20.94	0.00	3	3	0		0
CCDC150	CCDC150:p.Arg589His		13.83	0.00	2	2	0	0.00	1
MAP2	MAP2:p.Leu867Met	0.47	30.34	0.00	2	2	0		0
MAP2	MAP2:p.Leu867Arg	0.47	30.34	0.00	2	2	0		0
FJX1	FJX1:p.Ter438TrpextTer80		0.65	0.00	2	2	0		0
ATP7B	ATP7B:p.Ala1063Val		7.14	0.00	2	2	0	0.00	1
GPT2	GPT2:p.Gly203Asp		2.00	0.00	2	2	0		0
SMOX	SMOX:p.Gly249Asp		10.69	0.00	2	2	0	0.00	1
HELZ2	HELZ2:p.Ala1802Val		14.49	0.00	2	2	0		0
USP9Y	USP9Y:p.Ala2187Val		45.04	0.00	2	2	0		0
NBPF3	NBPF3:p.Phe429Cys		1.22	0.00	1	1	0		0
GRIK3	GRIK3:p.Arg801Trp		2.56	0.00	1	1	0	0.00	1
HFM1	HFM1:p.Ala1062Val		0.86	0.00	1	1	0		0
PHGDH	PHGDH:p.Ala255Val		1.45	0.00	1	1	0		0
GPR52	GPR52:p.His109Asp		20.01	0.00	1	1	0		0
LRATD1	LRATD1:p.Ala172Thr		5.20	0.00	1	1	0		0
CLRN1	CLRN1:p.Val47Ile		0.18	0.00	1	1	0		0
ANKRD33B	ANKRD33B:p.Gly364Ser		0.14	0.00	1	1	0		0
CFAP58	CFAP58:p.Ala478Thr		0.88	0.00	1	1	0		0
UBQLN3	UBQLN3:p.Ser554Asn		1.71	0.00	1	1	0	0.00	1
DNHD1	DNHD1:p.Arg1551Trp		14.74	0.00	1	1	0	0.00	1
CDC42BPG	CDC42BPG:p.Ala792Thr		0.08	0.00	1	1	0		0
PC	PC:p.Gly150Glu		9.93	0.00	1	1	0		0
IQSEC3	IQSEC3:p.Tyr1156Asn		2.64	0.00	1	1	0		0
SPTBN5	SPTBN5:p.Ala1719Val		11.40	0.00	1	1	0		0
CHRNB1	CHRNB1:p.His340Pro		5.12	0.00	1	1	0		0
MYO15B	MYO15B:p.Pro633His		27.21	0.00	1	1	0		0
LOXHD1	LOXHD1:p.Ala1280Thr		5.53	0.00	1	1	0		0
ITSN1	ITSN1:p.Glu1443Gly		91.12	0.00	1	1	0		0
SHROOM4	SHROOM4:p.Ala1419Val		11.76	0.00	1	1	0		0
RAP1GAP	RAP1GAP:p.Arg88His		0.30
CSMD2	CSMD2:p.Arg1116His		0.38
LRRC7	LRRC7:p.Val599Ile		1.74
LCE1B	LCE1B:p.Pro14Ser		0.00
PGLYRP4	PGLYRP4:p.Val288_Gly294del		0.00
DCST2	DCST2:p.Val9Leu		0.30
CHIT1	CHIT1:p.Gly60Asp		1.08
CNTN2	CNTN2:p.Gly965Asp		0.31
OBSCN	OBSCN:p.Pro7410Ser		4.10
KIF26B	KIF26B:p.Ala1734Asp		0.61
C2orf50	C2orf50:p.Arg85His		0.12
NTSR2	NTSR2:p.Arg287Cys		0.00
GPR148	GPR148:p.Leu203Pro		0.00
PPP1R1C	PPP1R1C:p.Ala12Val		4.29
MAP2	MAP2:p.Gly868AlafsTer38		30.34
CELSR3	CELSR3:p.Ala1792Thr		0.29
ERC2	ERC2:p.Lys866Asn		3.70
CNTN3	CNTN3:p.Glu452Asp		3.70
SI	SI:p.Thr587Ile		0.03
ZAR1	ZAR1:p.Ala233Val		0.00
DSPP	DSPP:p.Ser1223_Ser1261del		1.70
SLC9A3	SLC9A3:p.Ala50Val		1.07
H1-2	H1-2:p.Ala197_Lys201del		861.71
PRSS16	PRSS16:p.Ala55Asp		0.36
CCN6	CCN6:p.Leu246Met		0.45
FNDC1	FNDC1:p.Ala91Val		23.69
SP8	SP8:p.Ala148Val		0.00
HOXA13	HOXA13:p.Ala214Thr		0.01
TECPR1	TECPR1:p.Thr259HisfsTer77		16.12
VGF	VGF:p.Pro42Ser		0.30
RP1L1	RP1L1:p.Leu792Val		0.28
CNTNAP3	CNTNAP3:p.Ala1204Thr		1.23
HMCN2	HMCN2:p.Pro3777His		0.33
GTF3C5	GTF3C5:p.Glu496_Glu499del		24.01
DBH	DBH:p.His457Tyr		0.37
GPR158	GPR158:p.Ala106Val		19.76
RET	RET:p.Glu208Lys		0.08
GPRIN2	GPRIN2:p.Arg242Lys		0.00
C10orf71	C10orf71:p.Pro199Ser		0.00
DNTT	DNTT:p.Ala463Val		0.05
PITX3	PITX3:p.Gly224ArgfsTer38		0.34
C10orf120	C10orf120:p.Asp222Val		0.00
HMX2	HMX2:p.Ala145Thr		0.00
CTBP2	CTBP2:p.Pro424Ser		15.46
CFAP46	CFAP46:p.Ala2297Val		0.12
KRTAP5-4	KRTAP5-4:p.Gly34Ser		0.10
OR51S1	OR51S1:p.Pro61Ser		0.00
OR10AG1	OR10AG1:p.Leu256Ile		0.00
CCDC83	CCDC83:p.Pro16Gln		0.40
MUC19	MUC19:p.Ile626Asn		7.64
AMIGO2	AMIGO2:p.Trp243GlyfsTer9		6.06
TSPAN19	TSPAN19:p.Gly74Ser		0.63
PCDH8	PCDH8:p.Leu871Ile		0.03
NALCN	NALCN:p.Phe351Ser		0.05
CCDC168	CCDC168:p.Ser442Ile		0.14
SOX1	SOX1:p.Ala378Val		0.00
GRK1	GRK1:p.Ala510Val		0.00
ESR2	ESR2:p.Pro277Ser		1.88
SLC25A47	SLC25A47:p.Ala119Thr		0.21
AHNAK2	AHNAK2:p.Val2219Met		2.59
AGBL1	AGBL1:p.Leu29Pro		0.00
CASKIN1	CASKIN1:p.Gly905Asp		0.12
C16orf90	C16orf90:p.Gly26Val		0.20
HS3ST4	HS3ST4:p.Pro422Gln		0.08
IRX6	IRX6:p.Ala119Thr		2.44
PITPNM3	PITPNM3:p.Ala638Thr		1.03
NOS2	NOS2:p.Tyr491Ser		0.19
CACNG5	CACNG5:p.Ala183Thr		0.00
MYO15B	MYO15B:p.Pro634ArgfsTer43		27.21
TSPAN10	TSPAN10:p.Ala267Val		0.00
SERPINB11	SERPINB11:p.Ser40Gly		0.00
MUC16	MUC16:p.Gly12343Ser		0.05
OR7D4	OR7D4:p.Lys298Glu		0.00
DMKN	DMKN:p.Gly284Ser		0.12
CCDC8	CCDC8:p.Glu351Gln		0.02
SLC8A2	SLC8A2:p.Ala33Thr		0.01
SHANK1	SHANK1:p.Glu11Lys		1.57
SPEF1	SPEF1:p.Gln230Lys		0.27
DLGAP4	DLGAP4:p.Ala182Thr		71.20
KRTAP10-4	KRTAP10-4:p.Arg62Leu		0.00
KRTAP10-6	KRTAP10-6:p.Arg62Leu		0.09
FTCD	FTCD:p.Ala411Val		0.00
TMPRSS6	TMPRSS6:p.Pro387Ser		0.35
CACNA1I	CACNA1I:p.Cys1163Phe		0.02
MOV10L1	MOV10L1:p.Ser1024Arg		0.58
WWC3	WWC3:p.Gln239HisfsTer33		25.59
FRMPD3	FRMPD3:p.Arg811His		0.18
PASD1	PASD1:p.Asn22Lys		0.00

Ranked from highest to lowest tumor AF minus all-cell AF. All 13 candidates with coverage in both groups and a nonzero difference are shown (up to 20); zero/zero pairs are omitted. All cells includes tumor cells. Hover a bar for its value, read depth and AF difference. Zero AF has no visible bar.

Per-site aggregated allele frequency

Same, aggregated per genomic site (total depth and mutant reads across all cells).

Chrom	Pos	Ref	Alt	Total depth (DP)	Mutant reads (AD)	sc RNA-AF (all cells)	Cells covered	Cells w/ mutant	Malignant depth	sc RNA-AF (malignant)
chr6	31,356,732	T	A	41,796	1,803	0.04	4,107	1,317	180	0.11
chr19	41,861,129	T	C	28,198	7	0.00	3,966	7	129	0.00
chr6	32,584,213	T	G	7,676	974	0.13	1,375	532	3	0.00
chr19	5,896,456	G	A	3,744	4	0.00	1,858	4	24	0.00
chr6	158,818,090	G	A	1,937	3	0.00	1,317	3	58	0.02
chr19	33,512,646	C	T	999	0	0.00	761	0	8	0.00
chr19	36,114,384	G	A	877	0	0.00	706	0	11	0.00
chrX	153,596,058	C	T	661	1	0.00	567	1	1	0.00
chr7	133,274,996	G	T	588	75	0.13	503	72	52	0.29
chr16	642,155	G	A	519	0	0.00	432	0	7	0.00
chr2	70,088,660	G	A	516	0	0.00	456	0	2	0.00
chr10	119,872,535	C	T	418	0	0.00	387	0	13	0.00
chrX	119,399,652	C	A	382	0	0.00	342	0	18	0.00
chr2	131,071,917	G	A	363	0	0.00	328	0	7	0.00
chr10	32,911,945	C	T	332	0	0.00	260	0	26	0.00
chrX	66,032,555	T	C	249	0	0.00	204	0	0
chr3	194,628,498	A	C	238	1	0.00	207	1	16	0.00
chr22	46,793,673	G	A	234	0	0.00	226	0	6	0.00
chr19	41,331,110	C	T	184	0	0.00	177	0	7	0.00
chr12	66,137,988	C	T	179	0	0.00	171	0	8	0.00
chr6	24,716,285	G	A	170	0	0.00	163	0	9	0.00
chr1	68,137,918	A	G	159	0	0.00	137	0	4	0.00
chr20	32,474,634	G	A	157	0	0.00	137	0	2	0.00
chr10	49,107,771	C	T	156	0	0.00	133	0	12	0.00
chr19	48,739,550	G	A	134	0	0.00	97	0	1	0.00
chr6	112,115,912	C	T	124	0	0.00	111	0	11	0.00
chr4	153,466,443	G	A	116	0	0.00	112	0	7	0.00
chr14	101,980,529	G	A	116	34	0.29	112	34	9	0.44
chr6	63,698,534	C	T	115	0	0.00	113	0	4	0.00
chr7	77,196,965	C	A	115	0	0.00	105	0	0
chr17	41,757,708	G	A	111	1	0.01	92	1	3	0.00
chr17	42,562,753	G	A	106	0	0.00	101	0	1	0.00
chr19	2,248,347	G	A	106	0	0.00	103	0	7	0.00
chr9	97,910,412	C	T	102	6	0.06	96	6	1	0.00
chr1	23,863,264	G	A	98	0	0.00	84	0	0
chr3	180,957,830	G	A	95	1	0.01	91	1	2	0.00
chr3	9,933,190	C	T	81	0	0.00	78	0	1	0.00
chrX	30,251,362	C	T	80	0	0.00	68	0	3	0.00
chr2	135,782,799	A	T	78	0	0.00	76	0	2	0.00
chr19	35,644,310	G	A	77	0	0.00	74	0	0
chr1	112,449,129	G	A	75	0	0.00	72	0	1	0.00
chr4	151,014,497	G	A	75	0	0.00	73	0	4	0.00
chr20	21,333,992	G	T	73	0	0.00	72	0	5	0.00
chr7	75,542,874	C	T	69	0	0.00	65	0	3	0.00
chr8	91,070,400	A	T	69	0	0.00	65	0	4	0.00
chr1	37,998,037	G	A	66	0	0.00	63	0	0
chr15	25,355,924	C	T	66	0	0.00	65	0	2	0.00
chr15	50,736,188	C	T	65	0	0.00	63	0	3	0.00
chr19	30,005,450	G	A	63	2	0.03	61	2	0
chr1	116,393,693	G	A	62	0	0.00	61	0	0
chr1	85,200,575	C	A	61	0	0.00	58	0	13	0.00
chrX	70,146,758	T	C	61	0	0.00	60	0	1	0.00
chr14	23,477,324	G	A	59	0	0.00	58	0	3	0.00
chr17	82,096,423	C	T	58	0	0.00	55	0	2	0.00
chr2	200,477,702	G	A	55	0	0.00	55	0	1	0.00
chr17	9,250,589	G	A	52	0	0.00	51	0	0
chr16	50,782,427	G	A	51	0	0.00	49	0	1	0.00
chr2	151,463,616	G	A	50	0	0.00	50	0	2	0.00
chr7	151,218,156	G	C	50	0	0.00	46	0	3	0.00
chrX	75,071,554	C	T	50	0	0.00	47	0	0
chr4	118,805,905	G	A	49	0	0.00	44	0	3	0.00
chr17	44,321,193	G	A	47	0	0.00	45	0	1	0.00
chr17	7,390,414	C	T	45	0	0.00	45	0	1	0.00
chr12	101,757,282	C	A	43	0	0.00	39	0	0
chr1	171,566,740	C	T	41	0	0.00	41	0	4	0.00
chr2	95,087,493	G	A	41	0	0.00	40	0	2	0.00
chr1	171,566,725	C	T	39	0	0.00	39	0	4	0.00
chr6	7,402,878	G	A	39	0	0.00	39	0	0
chr20	1,937,414	C	T	38	0	0.00	37	0	0
chr2	97,841,867	C	T	37	0	0.00	36	0	3	0.00
chr3	37,094,793	C	T	36	0	0.00	35	0	0
chr6	46,856,758	T	C	36	0	0.00	33	0	0
chr19	51,704,376	C	G	36	0	0.00	34	0	3	0.00
chr19	54,454,640	G	A	35	0	0.00	35	0	1	0.00
chr5	138,391,529	C	T	34	0	0.00	34	0	1	0.00
chr18	79,253,493	G	A	32	0	0.00	32	0	2	0.00
chr3	149,071,430	G	A	30	0	0.00	30	0	1	0.00
chr12	122,035,418	G	A	28	0	0.00	27	0	4	0.00
chr10	72,692,176	C	G	27	0	0.00	27	0	2	0.00
chr13	24,490,765	C	T	27	0	0.00	27	0	3	0.00
chr1	31,269,238	G	T	26	0	0.00	26	0	1	0.00
chr2	171,813,470	A	G	26	9	0.35	25	9	0
chr16	53,267,414	C	T	26	0	0.00	23	0	0
chr15	96,332,299	G	T	25	0	0.00	24	0	0
chr11	5,603,535	G	A	24	0	0.00	23	0	0
chr12	52,951,767	G	T	24	0	0.00	24	0	0
chr20	3,800,858	A	C	24	0	0.00	23	0	0
chr1	19,086,238	G	A	23	0	0.00	23	0	1	0.00
chr8	89,769,919	G	A	23	0	0.00	22	0	0
chr19	38,600,136	C	T	23	0	0.00	23	0	1	0.00
chr19	46,704,586	C	T	23	0	0.00	22	0	0
chr6	43,547,657	T	G	22	0	0.00	20	0	2	0.00
chr8	143,792,353	C	T	22	0	0.00	22	0	0
chr11	46,680,250	C	T	22	0	0.00	22	0	0
chr12	53,059,092	C	T	22	0	0.00	21	0	2	0.00
chr14	74,509,748	C	T	21	0	0.00	21	0	3	0.00
chr16	30,766,754	G	A	21	0	0.00	21	0	1	0.00
chr18	6,859,875	C	T	21	1	0.05	20	1	4	0.00
chr2	219,235,853	C	T	20	0	0.00	20	0	2	0.00
chr11	596,963	C	T	20	0	0.00	19	0	3	0.00
chr11	117,290,530	G	A	20	0	0.00	20	0	1	0.00
chrX	10,079,773	T	A	19	0	0.00	18	0	3	0.00
chr11	61,132,089	G	A	18	0	0.00	18	0	1	0.00
chr13	110,677,056	C	T	18	0	0.00	18	0	0
chr20	56,397,461	G	A	18	0	0.00	18	0	0
chr2	24,697,778	C	T	17	0	0.00	17	0	1	0.00
chr3	136,151,340	G	A	17	0	0.00	17	0	1	0.00
chr7	128,323,541	C	T	17	0	0.00	17	0	3	0.00
chr15	73,270,080	G	A	17	0	0.00	17	0	2	0.00
chr17	44,092,504	G	A	17	0	0.00	17	0	1	0.00
chrX	118,393,056	C	T	17	0	0.00	17	0	1	0.00
chr10	98,429,609	A	C	16	0	0.00	16	0	0
chr17	19,867,354	C	A	16	0	0.00	16	0	0
chr19	52,384,818	G	T	16	5	0.31	15	5	3	0.33
chr1	19,162,493	C	T	15	0	0.00	15	0	0
chr6	110,228,933	G	A	15	0	0.00	15	0	0
chr12	111,644,377	C	T	15	0	0.00	15	0	0
chr17	1,585,992	C	T	15	0	0.00	15	0	0
chr17	5,007,293	G	A	15	0	0.00	14	0	0
chr3	155,853,606	G	A	14	0	0.00	14	0	1	0.00
chr8	55,805,019	C	T	14	0	0.00	14	0	1	0.00
chr19	57,979,767	C	T	14	0	0.00	14	0	0
chr3	15,645,183	T	G	13	1	0.08	13	1	0
chr3	100,451,756	A	T	13	2	0.15	12	2	0
chr12	100,072,803	G	A	13	0	0.00	13	0	1	0.00
chr19	13,136,403	C	T	13	0	0.00	13	0	0
chr19	49,117,940	C	T	13	0	0.00	13	0	1	0.00
chrX	119,591,043	C	T	13	0	0.00	13	0	1	0.00
chr1	150,498,578	G	A	12	0	0.00	12	0	1	0.00
chr3	13,317,776	C	T	12	0	0.00	12	0	0
chr11	110,164,385	G	A	12	0	0.00	12	0	0
chr2	31,260,890	A	C	11	0	0.00	10	0	0
chr5	179,137,772	C	T	11	0	0.00	11	0	1	0.00
chr7	36,419,267	A	T	11	0	0.00	11	0	0
chr12	6,029,448	T	C	11	0	0.00	10	0	0
chr1	91,716,387	C	T	10	0	0.00	10	0	0
chr2	38,075,262	G	A	10	0	0.00	9	0	0
chr3	171,167,148	C	T	10	0	0.00	10	0	2	0.00
chr4	88,658,489	G	A	10	0	0.00	10	0	1	0.00
chr6	154,827,180	C	T	10	0	0.00	10	0	0
chr19	16,157,681	G	T	9	0	0.00	9	0	0
chr1	23,362,762	G	C	8	3	0.38	8	3	2	1.00
chr1	235,777,088	C	T	8	0	0.00	8	0	0
chr9	128,995,422	G	A	8	0	0.00	8	0	1	0.00
chr13	95,083,250	G	A	8	0	0.00	8	0	2	0.00
chr16	5,090,135	C	T	8	0	0.00	8	0	0
chr16	66,963,365	C	T	8	0	0.00	8	0	1	0.00
chr3	77,607,853	C	A	7	6	0.86	7	6	0
chr3	129,502,728	G	A	7	0	0.00	7	0	0
chr8	99,861,923	C	T	7	0	0.00	7	0	0
chr15	71,994,488	T	A	7	0	0.00	7	0	0
chr19	39,176,660	G	A	7	0	0.00	7	0	1	0.00
chr22	38,085,373	C	T	7	0	0.00	7	0	2	0.00
chr1	27,549,621	C	T	6	0	0.00	6	0	0
chr6	43,186,384	G	T	6	0	0.00	6	0	0
chr14	72,978,146	G	A	6	0	0.00	6	0	0
chr18	45,925,851	C	T	6	0	0.00	6	0	0
chr18	79,714,886	G	T	6	0	0.00	6	0	0
chr2	216,432,770	G	C	5	0	0.00	5	0	0
chr3	112,925,190	G	A	5	0	0.00	5	0	0
chr17	63,389,536	C	T	5	0	0.00	5	0	0
chr19	47,701,906	C	T	5	0	0.00	5	0	0
chr1	2,374,508	C	T	4	0	0.00	4	0	1	0.00
chr2	196,847,081	G	A	4	0	0.00	4	0	0
chr8	144,054,726	G	A	4	0	0.00	4	0	0
chr13	95,552,892	G	A	4	0	0.00	1	0	0
chr15	42,775,355	G	C	4	0	0.00	4	0	0
chr19	884,936	C	T	4	0	0.00	4	0	0
chr19	16,517,273	C	T	4	0	0.00	4	0	2	0.00
chr19	40,213,624	C	T	4	0	0.00	4	0	0
chr2	160,013,371	C	A	3	0	0.00	3	0	1	0.00
chr4	56,315,442	C	T	3	0	0.00	3	0	1	0.00
chr6	152,334,011	G	A	3	0	0.00	3	0	0
chr16	426,308	C	T	3	0	0.00	3	0	0
chr16	57,567,987	C	T	3	0	0.00	3	0	0
chr17	74,562,846	C	T	3	0	0.00	3	0	0
chrX	134,425,272	G	A	3	0	0.00	3	0	0
chr2	196,712,215	G	A	2	0	0.00	2	0	1	0.00
chr2	209,694,769	C	A	2	0	0.00	2	0	0
chr2	209,694,770	T	G	2	0	0.00	2	0	0
chr11	35,619,949	A	G	2	0	0.00	2	0	0
chr13	51,944,164	G	A	2	0	0.00	2	0	1	0.00
chr16	46,909,715	G	A	2	0	0.00	2	0	0
chr20	4,182,225	G	A	2	0	0.00	2	0	1	0.00
chr20	63,563,417	G	A	2	0	0.00	2	0	0
chrY	12,843,185	C	T	2	0	0.00	2	0	0
chr1	21,480,128	T	G	1	0	0.00	1	0	0
chr1	36,805,151	G	A	1	0	0.00	1	0	1	0.00
chr1	91,314,016	G	A	1	0	0.00	1	0	0
chr1	119,735,415	C	T	1	0	0.00	1	0	0
chr1	174,448,436	C	G	1	0	0.00	1	0	0
chr2	14,634,493	G	A	1	0	0.00	1	0	0
chr3	150,972,570	C	T	1	0	0.00	1	0	0
chr5	10,649,718	G	A	1	0	0.00	1	0	0
chr10	104,392,299	G	A	1	0	0.00	1	0	0
chr11	5,507,898	C	T	1	0	0.00	1	0	1	0.00
chr11	6,545,590	C	T	1	0	0.00	1	0	1	0.00
chr11	64,834,305	C	T	1	0	0.00	1	0	0
chr11	66,871,353	C	T	1	0	0.00	1	0	0
chr12	174,950	T	A	1	0	0.00	1	0	0
chr15	41,872,311	G	A	1	0	0.00	1	0	0
chr17	7,454,495	A	C	1	0	0.00	1	0	0
chr17	75,589,955	C	A	1	0	0.00	1	0	0
chr18	46,541,851	C	T	1	0	0.00	1	0	0
chr21	33,875,508	A	G	1	0	0.00	1	0	0
chrX	50,596,921	G	A	1	0	0.00	1	0	0

Tumor heterogeneity & subclones

Tumor subclone structure, an overall heterogeneity score, and how each neoantigen's presence and expression vary across subclones.

Subclone count, heterogeneity score & largest subclone

Number of tumor subclones, an ITH (heterogeneity) score, and the size of the largest subclone.

211

Malignant cells

Subclones

1.04

ITH (Shannon)

44.5%

Largest subclone

Toggle between the whole sample and a zoom into the tumour tissue type — the Fibroblast compartment the cancer arises in (same embedding, filtered). Hover a point for its label.

Neoantigen clonal vs subclonal status

Each neoantigen labeled clonal (present across subclones) vs subclonal (in only some).

Gene	Mutation	Subclones covered	Subclones expressed	Clonality
EXOC4	EXOC4:p.Ser34Ile	2	2	clonal
DYNC1H1	DYNC1H1:p.Val314Ile	2	2	clonal
HLA-B	HLA-B:p.Glu100Val	3	2	subclonal
EZR	EZR:p.Pro2Ser	2	1	subclonal
SYDE2	SYDE2:p.Gly141Val	2	0	not_expressed
FAM168B	FAM168B:p.Ala31Val	2	0	not_expressed
TMEM44	TMEM44:p.Leu50Arg	2	0	not_expressed
C6orf62	C6orf62:p.Pro57Ser	2	0	not_expressed
LAMA4	LAMA4:p.Gly1688Asp	2	0	not_expressed
ITGB1	ITGB1:p.Gly550Asp	2	0	not_expressed
VSTM4	VSTM4:p.Ala94Thr	2	0	not_expressed
MCMBP	MCMBP:p.Gly17Glu	2	0	not_expressed
NDUFA11	NDUFA11:p.Arg104Cys	2	0	not_expressed
POLR2I	POLR2I:p.Ala48Val	2	0	not_expressed
RPS19	RPS19:p.Val30Ala	3	0	not_expressed
SLC25A43	SLC25A43:p.Ser83Arg	2	0	not_expressed
MORN1	MORN1:p.Cys196Tyr	0	0	insufficient
UBR4	UBR4:p.Ala4907Val	0	0	insufficient
UBR4	UBR4:p.Arg1628Gln	0	0	insufficient
NBPF3	NBPF3:p.Phe429Cys	0	0	insufficient
ZNF436	ZNF436:p.Ser207Cys	0	0	insufficient
FUCA1	FUCA1:p.Arg178Cys	0	0	insufficient
AHDC1	AHDC1:p.Arg832His	0	0	insufficient
SNRNP40	SNRNP40:p.Arg260Ser	0	0	insufficient
GRIK3	GRIK3:p.Arg801Trp	0	0	insufficient
FHL3	FHL3:p.Pro143Ser	0	0	insufficient
WLS	WLS:p.Trp460Arg	1	0	insufficient
HFM1	HFM1:p.Ala1062Val	0	0	insufficient
TGFBR3	TGFBR3:p.Cys572Tyr	0	0	insufficient
CTTNBP2NL	CTTNBP2NL:p.Arg96His	0	0	insufficient
ATP1A1	ATP1A1:p.Glu544Lys	0	0	insufficient
PHGDH	PHGDH:p.Ala255Val	0	0	insufficient
TARS2	TARS2:p.Ala439Thr	0	0	insufficient
PRRC2C	PRRC2C:p.Ala2147Val	1	0	insufficient
PRRC2C	PRRC2C:p.Thr2152Ile	1	0	insufficient
GPR52	GPR52:p.His109Asp	0	0	insufficient
LYST	LYST:p.Gly1812Asp	0	0	insufficient
LRATD1	LRATD1:p.Ala172Thr	0	0	insufficient
NCOA1	NCOA1:p.Ala310Val	0	0	insufficient
EHD3	EHD3:p.Asn295His	0	0	insufficient
CYP1B1	CYP1B1:p.Arg43Trp	0	0	insufficient
PCBP1	PCBP1:p.Arg306His	0	0	insufficient
MRPS5	MRPS5:p.Ser386Phe	0	0	insufficient
TMEM131	TMEM131:p.Ser224Asn	1	0	insufficient
UBXN4	UBXN4:p.Lys480Met	0	0	insufficient
RIF1	RIF1:p.Val1366Ile	0	0	insufficient
PLA2R1	PLA2R1:p.Trp519Leu	0	0	insufficient
SLC25A12	SLC25A12:p.Ile347Thr	0	0	insufficient
CCDC150	CCDC150:p.Arg589His	0	0	insufficient
PGAP1	PGAP1:p.Thr691Met	0	0	insufficient
SPATS2L	SPATS2L:p.Ala450Thr	0	0	insufficient
MAP2	MAP2:p.Leu867Met	0	0	insufficient
MAP2	MAP2:p.Leu867Arg	0	0	insufficient
SMARCAL1	SMARCAL1:p.Gly463Arg	0	0	insufficient
ANKZF1	ANKZF1:p.Ala650Val	0	0	insufficient
IL17RC	IL17RC:p.Ala587Val	0	0	insufficient
NUP210	NUP210:p.Ala1857Thr	0	0	insufficient
BTD	BTD:p.Phe423Val	0	0	insufficient
LRRFIP2	LRRFIP2:p.Arg345Gln	0	0	insufficient
ROBO2	ROBO2:p.Asn1068Lys	0	0	insufficient
LNP1	LNP1:p.His65Leu	0	0	insufficient
CD200R1	CD200R1:p.Pro258Leu	0	0	insufficient
IFT122	IFT122:p.Arg798His	0	0	insufficient
MSL2	MSL2:p.Ala514Val	0	0	insufficient
HLTF	HLTF:p.Pro239Leu	0	0	insufficient
CLRN1	CLRN1:p.Val47Ile	0	0	insufficient
SLC33A1	SLC33A1:p.Ala131Val	0	0	insufficient
TNIK	TNIK:p.Arg299His	0	0	insufficient
FXR1	FXR1:p.Gly298Arg	0	0	insufficient
CRACD	CRACD:p.Ala647Val	0	0	insufficient
HERC3	HERC3:p.Glu382Lys	0	0	insufficient
SEC24D	SEC24D:p.Ala284Val	0	0	insufficient
LRBA	LRBA:p.Ala49Val	1	0	insufficient
TMEM131L	TMEM131L:p.Ala16Thr	1	0	insufficient
ANKRD33B	ANKRD33B:p.Gly364Ser	0	0	insufficient
KDM3B	KDM3B:p.Pro633Ser	0	0	insufficient
ADAMTS2	ADAMTS2:p.Asp650Asn	0	0	insufficient
RIOK1	RIOK1:p.Glu250Lys	0	0	insufficient
HLA-DRB1	HLA-DRB1:p.Tyr89Ser	0	0	insufficient
CUL9	CUL9:p.Asp394Tyr	0	0	insufficient
XPO5	XPO5:p.Lys704Thr	0	0	insufficient
ADGRF5	ADGRF5:p.Asn1279Ser	0	0	insufficient
PHF3	PHF3:p.Arg971Trp	1	0	insufficient
CDC40	CDC40:p.Val507Ile	0	0	insufficient
SYNE1	SYNE1:p.Ala4264Val	0	0	insufficient
SCAF8	SCAF8:p.Pro694Ser	0	0	insufficient
ANLN	ANLN:p.Ser553Cys	0	0	insufficient
HIP1	HIP1:p.Gly956Asp	0	0	insufficient
FGL2	FGL2:p.Asp212Tyr	0	0	insufficient
RBM28	RBM28:p.Ala464Thr	0	0	insufficient
ABCF2	ABCF2:p.Asp421Glu	0	0	insufficient
TGS1	TGS1:p.Ala709Val	0	0	insufficient
RIPK2	RIPK2:p.Asp211Asn	0	0	insufficient
OTUD6B	OTUD6B:p.Thr6Ser	1	0	insufficient
VPS13B	VPS13B:p.Ser3731Phe	0	0	insufficient
SCRIB	SCRIB:p.Ala1461Thr	0	0	insufficient
OPLAH	OPLAH:p.Pro841Ser	0	0	insufficient
TRMO	TRMO:p.Gly205Glu	0	0	insufficient
NUP188	NUP188:p.Ala1087Thr	0	0	insufficient
MCU	MCU:p.Leu9Val	0	0	insufficient
HPS1	HPS1:p.Phe301Val	0	0	insufficient
CFAP58	CFAP58:p.Ala478Thr	0	0	insufficient
PHRF1	PHRF1:p.Pro221Ser	0	0	insufficient
UBQLN3	UBQLN3:p.Ser554Asn	0	0	insufficient
TRIM6	TRIM6:p.Ala103Thr	0	0	insufficient
DNHD1	DNHD1:p.Arg1551Trp	0	0	insufficient
FJX1	FJX1:p.Ter438TrpextTer80	0	0	insufficient
ARHGAP1	ARHGAP1:p.Ala285Thr	0	0	insufficient
VPS37C	VPS37C:p.Pro267Ser	0	0	insufficient
CDC42BPG	CDC42BPG:p.Ala792Thr	0	0	insufficient
PC	PC:p.Gly150Glu	0	0	insufficient
ZC3H12C	ZC3H12C:p.Glu434Lys	0	0	insufficient
BACE1	BACE1:p.Arg408Trp	0	0	insufficient
IQSEC3	IQSEC3:p.Tyr1156Asn	0	0	insufficient
VWF	VWF:p.Glu954Gly	0	0	insufficient
KRT18	KRT18:p.Ala287Ser	0	0	insufficient
TNS2	TNS2:p.Ala484Val	0	0	insufficient
TMBIM4	TMBIM4:p.Arg230Gln	1	0	insufficient
BLTP3B	BLTP3B:p.Ala473Val	0	0	insufficient
GNPTAB	GNPTAB:p.Ala1122Ser	0	0	insufficient
BRAP	BRAP:p.Arg534His	0	0	insufficient
BCL7A	BCL7A:p.Asp88Asn	0	0	insufficient
PARP4	PARP4:p.Ala373Thr	1	0	insufficient
ATP7B	ATP7B:p.Ala1063Val	0	0	insufficient
ABCC4	ABCC4:p.Ala859Val	0	0	insufficient
CLDN10	CLDN10:p.Ala47Thr	0	0	insufficient
CARS2	CARS2:p.Ala235Thr	0	0	insufficient
NGDN	NGDN:p.Ala280Thr	0	0	insufficient
ZFYVE1	ZFYVE1:p.Ala503Val	0	0	insufficient
LTBP2	LTBP2:p.Gly1088Asp	1	0	insufficient
UBE3A	UBE3A:p.Asp698Asn	0	0	insufficient
SPTBN5	SPTBN5:p.Ala1719Val	0	0	insufficient
TTBK2	TTBK2:p.Pro593Arg	0	0	insufficient
SPPL2A	SPPL2A:p.Gly282Asp	0	0	insufficient
MYO9A	MYO9A:p.Asp523Val	0	0	insufficient
NEO1	NEO1:p.Met855Ile	0	0	insufficient
NR2F2	NR2F2:p.Gly65Val	0	0	insufficient
RAB11FIP3	RAB11FIP3:p.Ala101Val	0	0	insufficient
MCRIP2	MCRIP2:p.Glu30Lys	1	0	insufficient
EEF2KMT	EEF2KMT:p.Ala231Thr	0	0	insufficient
RNF40	RNF40:p.Gly436Glu	0	0	insufficient
GPT2	GPT2:p.Gly203Asp	0	0	insufficient
CYLD	CYLD:p.Gly596Asp	0	0	insufficient
CHD9	CHD9:p.Arg1481Trp	0	0	insufficient
ADGRG5	ADGRG5:p.Ala318Val	0	0	insufficient
CES3	CES3:p.Ala90Val	0	0	insufficient
SLC43A2	SLC43A2:p.Val380Ile	0	0	insufficient
KIF1C	KIF1C:p.Glu456Lys	0	0	insufficient
PLSCR3	PLSCR3:p.Gly287Ser	0	0	insufficient
CHRNB1	CHRNB1:p.His340Pro	0	0	insufficient
STX8	STX8:p.Pro234Ser	0	0	insufficient
ULK2	ULK2:p.Val22Leu	0	0	insufficient
JUP	JUP:p.Ala617Val	0	0	insufficient
COASY	COASY:p.Gly44Asp	0	0	insufficient
HDAC5	HDAC5:p.Arg266Cys	0	0	insufficient
SLC25A39	SLC25A39:p.Arg186Trp	0	0	insufficient
TANC2	TANC2:p.Arg1015Trp	0	0	insufficient
CD300H	CD300H:p.Ser157Asn	0	0	insufficient
MYO15B	MYO15B:p.Pro633His	0	0	insufficient
FASN	FASN:p.Gly8Asp	0	0	insufficient
ARHGAP28	ARHGAP28:p.Ala235Val	1	0	insufficient
EPG5	EPG5:p.Ala869Thr	0	0	insufficient
LOXHD1	LOXHD1:p.Ala1280Thr	0	0	insufficient
ATP9B	ATP9B:p.Arg407His	0	0	insufficient
CTDP1	CTDP1:p.Gly476Cys	0	0	insufficient
MED16	MED16:p.Val318Met	0	0	insufficient
SF3A2	SF3A2:p.Gly399Glu	1	0	insufficient
NACC1	NACC1:p.Thr373Ile	0	0	insufficient
HSH2D	HSH2D:p.Ala316Ser	0	0	insufficient
C19orf44	C19orf44:p.Ala649Val	0	0	insufficient
URI1	URI1:p.Asp153Asn	0	0	insufficient
PEPD	PEPD:p.Gly50Ser	1	0	insufficient
ETV2	ETV2:p.Gly264Asp	0	0	insufficient
MAP4K1	MAP4K1:p.Gly517Arg	0	0	insufficient
PAK4	PAK4:p.Gly477Asp	0	0	insufficient
MAP3K10	MAP3K10:p.Arg649Trp	0	0	insufficient
TGFB1	TGFB1:p.Arg372His	1	0	insufficient
PRKD2	PRKD2:p.Arg192His	0	0	insufficient
BICRA	BICRA:p.Arg1392Cys	0	0	insufficient
RASIP1	RASIP1:p.Ala78Val	0	0	insufficient
LIN7B	LIN7B:p.Pro175Leu	0	0	insufficient
SPACA6	SPACA6:p.Ser279Arg	0	0	insufficient
ZNF880	ZNF880:p.Cys413Phe	1	1	insufficient
LENG8	LENG8:p.Ala213Thr	0	0	insufficient
ZNF606	ZNF606:p.Gly305Ser	0	0	insufficient
SIRPA	SIRPA:p.Ala454Val	0	0	insufficient
CDC25B	CDC25B:p.Lys192Thr	0	0	insufficient
SMOX	SMOX:p.Gly249Asp	0	0	insufficient
XRN2	XRN2:p.Gly375Trp	0	0	insufficient
NOL4L	NOL4L:p.Arg270Trp	0	0	insufficient
CSTF1	CSTF1:p.Ala142Thr	0	0	insufficient
HELZ2	HELZ2:p.Ala1802Val	0	0	insufficient
ITSN1	ITSN1:p.Glu1443Gly	0	0	insufficient
BAIAP2L2	BAIAP2L2:p.Gly506Asp	0	0	insufficient
TBC1D22A	TBC1D22A:p.Ala98Thr	1	0	insufficient
WWC3	WWC3:p.Tyr240Asn	0	0	insufficient
MAGEB1	MAGEB1:p.Ala290Val	0	0	insufficient
SHROOM4	SHROOM4:p.Ala1419Val	0	0	insufficient
VSIG4	VSIG4:p.Ile203Val	0	0	insufficient
IGBP1	IGBP1:p.Ile203Thr	0	0	insufficient
ABCB7	ABCB7:p.Gly388Ser	0	0	insufficient
WDR44	WDR44:p.Ala204Val	0	0	insufficient
NKRF	NKRF:p.Val221Ile	0	0	insufficient
PHF6	PHF6:p.Arg347Gln	0	0	insufficient
CCNQ	CCNQ:p.Gly81Asp	0	0	insufficient
USP9Y	USP9Y:p.Ala2187Val	0	0	insufficient
RAP1GAP	RAP1GAP:p.Arg88His			N/A
CSMD2	CSMD2:p.Arg1116His			N/A
LRRC7	LRRC7:p.Val599Ile			N/A
LCE1B	LCE1B:p.Pro14Ser			N/A
PGLYRP4	PGLYRP4:p.Val288_Gly294del			N/A
DCST2	DCST2:p.Val9Leu			N/A
CHIT1	CHIT1:p.Gly60Asp			N/A
CNTN2	CNTN2:p.Gly965Asp			N/A
OBSCN	OBSCN:p.Pro7410Ser			N/A
KIF26B	KIF26B:p.Ala1734Asp			N/A
C2orf50	C2orf50:p.Arg85His			N/A
NTSR2	NTSR2:p.Arg287Cys			N/A
GPR148	GPR148:p.Leu203Pro			N/A
PPP1R1C	PPP1R1C:p.Ala12Val			N/A
MAP2	MAP2:p.Gly868AlafsTer38			N/A
CELSR3	CELSR3:p.Ala1792Thr			N/A
ERC2	ERC2:p.Lys866Asn			N/A
CNTN3	CNTN3:p.Glu452Asp			N/A
SI	SI:p.Thr587Ile			N/A
ZAR1	ZAR1:p.Ala233Val			N/A
DSPP	DSPP:p.Ser1223_Ser1261del			N/A
SLC9A3	SLC9A3:p.Ala50Val			N/A
H1-2	H1-2:p.Ala197_Lys201del			N/A
PRSS16	PRSS16:p.Ala55Asp			N/A
CCN6	CCN6:p.Leu246Met			N/A
FNDC1	FNDC1:p.Ala91Val			N/A
SP8	SP8:p.Ala148Val			N/A
HOXA13	HOXA13:p.Ala214Thr			N/A
TECPR1	TECPR1:p.Thr259HisfsTer77			N/A
VGF	VGF:p.Pro42Ser			N/A
RP1L1	RP1L1:p.Leu792Val			N/A
CNTNAP3	CNTNAP3:p.Ala1204Thr			N/A
HMCN2	HMCN2:p.Pro3777His			N/A
GTF3C5	GTF3C5:p.Glu496_Glu499del			N/A
DBH	DBH:p.His457Tyr			N/A
GPR158	GPR158:p.Ala106Val			N/A
RET	RET:p.Glu208Lys			N/A
GPRIN2	GPRIN2:p.Arg242Lys			N/A
C10orf71	C10orf71:p.Pro199Ser			N/A
DNTT	DNTT:p.Ala463Val			N/A
PITX3	PITX3:p.Gly224ArgfsTer38			N/A
C10orf120	C10orf120:p.Asp222Val			N/A
HMX2	HMX2:p.Ala145Thr			N/A
CTBP2	CTBP2:p.Pro424Ser			N/A
CFAP46	CFAP46:p.Ala2297Val			N/A
KRTAP5-4	KRTAP5-4:p.Gly34Ser			N/A
OR51S1	OR51S1:p.Pro61Ser			N/A
OR10AG1	OR10AG1:p.Leu256Ile			N/A
CCDC83	CCDC83:p.Pro16Gln			N/A
MUC19	MUC19:p.Ile626Asn			N/A
AMIGO2	AMIGO2:p.Trp243GlyfsTer9			N/A
TSPAN19	TSPAN19:p.Gly74Ser			N/A
PCDH8	PCDH8:p.Leu871Ile			N/A
NALCN	NALCN:p.Phe351Ser			N/A
CCDC168	CCDC168:p.Ser442Ile			N/A
SOX1	SOX1:p.Ala378Val			N/A
GRK1	GRK1:p.Ala510Val			N/A
ESR2	ESR2:p.Pro277Ser			N/A
SLC25A47	SLC25A47:p.Ala119Thr			N/A
AHNAK2	AHNAK2:p.Val2219Met			N/A
AGBL1	AGBL1:p.Leu29Pro			N/A
CASKIN1	CASKIN1:p.Gly905Asp			N/A
C16orf90	C16orf90:p.Gly26Val			N/A
HS3ST4	HS3ST4:p.Pro422Gln			N/A
IRX6	IRX6:p.Ala119Thr			N/A
PITPNM3	PITPNM3:p.Ala638Thr			N/A
NOS2	NOS2:p.Tyr491Ser			N/A
CACNG5	CACNG5:p.Ala183Thr			N/A
MYO15B	MYO15B:p.Pro634ArgfsTer43			N/A
TSPAN10	TSPAN10:p.Ala267Val			N/A
SERPINB11	SERPINB11:p.Ser40Gly			N/A
MUC16	MUC16:p.Gly12343Ser			N/A
OR7D4	OR7D4:p.Lys298Glu			N/A
DMKN	DMKN:p.Gly284Ser			N/A
CCDC8	CCDC8:p.Glu351Gln			N/A
SLC8A2	SLC8A2:p.Ala33Thr			N/A
SHANK1	SHANK1:p.Glu11Lys			N/A
SPEF1	SPEF1:p.Gln230Lys			N/A
DLGAP4	DLGAP4:p.Ala182Thr			N/A
KRTAP10-4	KRTAP10-4:p.Arg62Leu			N/A
KRTAP10-6	KRTAP10-6:p.Arg62Leu			N/A
FTCD	FTCD:p.Ala411Val			N/A
TMPRSS6	TMPRSS6:p.Pro387Ser			N/A
CACNA1I	CACNA1I:p.Cys1163Phe			N/A
MOV10L1	MOV10L1:p.Ser1024Arg			N/A
WWC3	WWC3:p.Gln239HisfsTer33			N/A
FRMPD3	FRMPD3:p.Arg811His			N/A
PASD1	PASD1:p.Asn22Lys			N/A

Per-neoantigen × per-subclone AF and expression grid

The full grid: for every neoantigen × every subclone, its RNA allele frequency and source-gene expression.

Gene	Mutation	Clonality	Subclones covered	Subclones expressed	Mean expr (expressed)
HLA-B	HLA-B:p.Glu100Val	subclonal	3	2	0.63
EXOC4	EXOC4:p.Ser34Ile	clonal	2	2	2.05
DYNC1H1	DYNC1H1:p.Val314Ile	clonal	2	2	1.28
EZR	EZR:p.Pro2Ser	subclonal	2	1	0.52
ZNF880	ZNF880:p.Cys413Phe	insufficient	1	1	0.09
MORN1	MORN1:p.Cys196Tyr	insufficient	0	0
UBR4	UBR4:p.Ala4907Val	insufficient	0	0
UBR4	UBR4:p.Arg1628Gln	insufficient	0	0
NBPF3	NBPF3:p.Phe429Cys	insufficient	0	0
ZNF436	ZNF436:p.Ser207Cys	insufficient	0	0
FUCA1	FUCA1:p.Arg178Cys	insufficient	0	0
AHDC1	AHDC1:p.Arg832His	insufficient	0	0
SNRNP40	SNRNP40:p.Arg260Ser	insufficient	0	0
GRIK3	GRIK3:p.Arg801Trp	insufficient	0	0
FHL3	FHL3:p.Pro143Ser	insufficient	0	0
WLS	WLS:p.Trp460Arg	insufficient	1	0
SYDE2	SYDE2:p.Gly141Val	not_expressed	2	0
HFM1	HFM1:p.Ala1062Val	insufficient	0	0
TGFBR3	TGFBR3:p.Cys572Tyr	insufficient	0	0
CTTNBP2NL	CTTNBP2NL:p.Arg96His	insufficient	0	0
ATP1A1	ATP1A1:p.Glu544Lys	insufficient	0	0
PHGDH	PHGDH:p.Ala255Val	insufficient	0	0
TARS2	TARS2:p.Ala439Thr	insufficient	0	0
PRRC2C	PRRC2C:p.Ala2147Val	insufficient	1	0
PRRC2C	PRRC2C:p.Thr2152Ile	insufficient	1	0
GPR52	GPR52:p.His109Asp	insufficient	0	0
LYST	LYST:p.Gly1812Asp	insufficient	0	0
LRATD1	LRATD1:p.Ala172Thr	insufficient	0	0
NCOA1	NCOA1:p.Ala310Val	insufficient	0	0
EHD3	EHD3:p.Asn295His	insufficient	0	0
CYP1B1	CYP1B1:p.Arg43Trp	insufficient	0	0
PCBP1	PCBP1:p.Arg306His	insufficient	0	0
MRPS5	MRPS5:p.Ser386Phe	insufficient	0	0
TMEM131	TMEM131:p.Ser224Asn	insufficient	1	0
FAM168B	FAM168B:p.Ala31Val	not_expressed	2	0
UBXN4	UBXN4:p.Lys480Met	insufficient	0	0
RIF1	RIF1:p.Val1366Ile	insufficient	0	0
PLA2R1	PLA2R1:p.Trp519Leu	insufficient	0	0
SLC25A12	SLC25A12:p.Ile347Thr	insufficient	0	0
CCDC150	CCDC150:p.Arg589His	insufficient	0	0
PGAP1	PGAP1:p.Thr691Met	insufficient	0	0
SPATS2L	SPATS2L:p.Ala450Thr	insufficient	0	0
MAP2	MAP2:p.Leu867Met	insufficient	0	0
MAP2	MAP2:p.Leu867Arg	insufficient	0	0
SMARCAL1	SMARCAL1:p.Gly463Arg	insufficient	0	0
ANKZF1	ANKZF1:p.Ala650Val	insufficient	0	0
IL17RC	IL17RC:p.Ala587Val	insufficient	0	0
NUP210	NUP210:p.Ala1857Thr	insufficient	0	0
BTD	BTD:p.Phe423Val	insufficient	0	0
LRRFIP2	LRRFIP2:p.Arg345Gln	insufficient	0	0
ROBO2	ROBO2:p.Asn1068Lys	insufficient	0	0
LNP1	LNP1:p.His65Leu	insufficient	0	0
CD200R1	CD200R1:p.Pro258Leu	insufficient	0	0
IFT122	IFT122:p.Arg798His	insufficient	0	0
MSL2	MSL2:p.Ala514Val	insufficient	0	0
HLTF	HLTF:p.Pro239Leu	insufficient	0	0
CLRN1	CLRN1:p.Val47Ile	insufficient	0	0
SLC33A1	SLC33A1:p.Ala131Val	insufficient	0	0
TNIK	TNIK:p.Arg299His	insufficient	0	0
FXR1	FXR1:p.Gly298Arg	insufficient	0	0
TMEM44	TMEM44:p.Leu50Arg	not_expressed	2	0
CRACD	CRACD:p.Ala647Val	insufficient	0	0
HERC3	HERC3:p.Glu382Lys	insufficient	0	0
SEC24D	SEC24D:p.Ala284Val	insufficient	0	0
LRBA	LRBA:p.Ala49Val	insufficient	1	0
TMEM131L	TMEM131L:p.Ala16Thr	insufficient	1	0
ANKRD33B	ANKRD33B:p.Gly364Ser	insufficient	0	0
KDM3B	KDM3B:p.Pro633Ser	insufficient	0	0
ADAMTS2	ADAMTS2:p.Asp650Asn	insufficient	0	0
RIOK1	RIOK1:p.Glu250Lys	insufficient	0	0
C6orf62	C6orf62:p.Pro57Ser	not_expressed	2	0
HLA-DRB1	HLA-DRB1:p.Tyr89Ser	insufficient	0	0
CUL9	CUL9:p.Asp394Tyr	insufficient	0	0
XPO5	XPO5:p.Lys704Thr	insufficient	0	0
ADGRF5	ADGRF5:p.Asn1279Ser	insufficient	0	0
PHF3	PHF3:p.Arg971Trp	insufficient	1	0
CDC40	CDC40:p.Val507Ile	insufficient	0	0
LAMA4	LAMA4:p.Gly1688Asp	not_expressed	2	0
SYNE1	SYNE1:p.Ala4264Val	insufficient	0	0
SCAF8	SCAF8:p.Pro694Ser	insufficient	0	0
ANLN	ANLN:p.Ser553Cys	insufficient	0	0
HIP1	HIP1:p.Gly956Asp	insufficient	0	0
FGL2	FGL2:p.Asp212Tyr	insufficient	0	0
RBM28	RBM28:p.Ala464Thr	insufficient	0	0
ABCF2	ABCF2:p.Asp421Glu	insufficient	0	0
TGS1	TGS1:p.Ala709Val	insufficient	0	0
RIPK2	RIPK2:p.Asp211Asn	insufficient	0	0
OTUD6B	OTUD6B:p.Thr6Ser	insufficient	1	0
VPS13B	VPS13B:p.Ser3731Phe	insufficient	0	0
SCRIB	SCRIB:p.Ala1461Thr	insufficient	0	0
OPLAH	OPLAH:p.Pro841Ser	insufficient	0	0
TRMO	TRMO:p.Gly205Glu	insufficient	0	0
NUP188	NUP188:p.Ala1087Thr	insufficient	0	0
ITGB1	ITGB1:p.Gly550Asp	not_expressed	2	0
VSTM4	VSTM4:p.Ala94Thr	not_expressed	2	0
MCU	MCU:p.Leu9Val	insufficient	0	0
HPS1	HPS1:p.Phe301Val	insufficient	0	0
CFAP58	CFAP58:p.Ala478Thr	insufficient	0	0
MCMBP	MCMBP:p.Gly17Glu	not_expressed	2	0
PHRF1	PHRF1:p.Pro221Ser	insufficient	0	0
UBQLN3	UBQLN3:p.Ser554Asn	insufficient	0	0
TRIM6	TRIM6:p.Ala103Thr	insufficient	0	0
DNHD1	DNHD1:p.Arg1551Trp	insufficient	0	0
FJX1	FJX1:p.Ter438TrpextTer80	insufficient	0	0
ARHGAP1	ARHGAP1:p.Ala285Thr	insufficient	0	0
VPS37C	VPS37C:p.Pro267Ser	insufficient	0	0
CDC42BPG	CDC42BPG:p.Ala792Thr	insufficient	0	0
PC	PC:p.Gly150Glu	insufficient	0	0
ZC3H12C	ZC3H12C:p.Glu434Lys	insufficient	0	0
BACE1	BACE1:p.Arg408Trp	insufficient	0	0
IQSEC3	IQSEC3:p.Tyr1156Asn	insufficient	0	0
VWF	VWF:p.Glu954Gly	insufficient	0	0
KRT18	KRT18:p.Ala287Ser	insufficient	0	0
TNS2	TNS2:p.Ala484Val	insufficient	0	0
TMBIM4	TMBIM4:p.Arg230Gln	insufficient	1	0
BLTP3B	BLTP3B:p.Ala473Val	insufficient	0	0
GNPTAB	GNPTAB:p.Ala1122Ser	insufficient	0	0
BRAP	BRAP:p.Arg534His	insufficient	0	0
BCL7A	BCL7A:p.Asp88Asn	insufficient	0	0
PARP4	PARP4:p.Ala373Thr	insufficient	1	0
ATP7B	ATP7B:p.Ala1063Val	insufficient	0	0
ABCC4	ABCC4:p.Ala859Val	insufficient	0	0
CLDN10	CLDN10:p.Ala47Thr	insufficient	0	0
CARS2	CARS2:p.Ala235Thr	insufficient	0	0
NGDN	NGDN:p.Ala280Thr	insufficient	0	0
ZFYVE1	ZFYVE1:p.Ala503Val	insufficient	0	0
LTBP2	LTBP2:p.Gly1088Asp	insufficient	1	0
UBE3A	UBE3A:p.Asp698Asn	insufficient	0	0
SPTBN5	SPTBN5:p.Ala1719Val	insufficient	0	0
TTBK2	TTBK2:p.Pro593Arg	insufficient	0	0
SPPL2A	SPPL2A:p.Gly282Asp	insufficient	0	0
MYO9A	MYO9A:p.Asp523Val	insufficient	0	0
NEO1	NEO1:p.Met855Ile	insufficient	0	0
NR2F2	NR2F2:p.Gly65Val	insufficient	0	0
RAB11FIP3	RAB11FIP3:p.Ala101Val	insufficient	0	0
MCRIP2	MCRIP2:p.Glu30Lys	insufficient	1	0
EEF2KMT	EEF2KMT:p.Ala231Thr	insufficient	0	0
RNF40	RNF40:p.Gly436Glu	insufficient	0	0
GPT2	GPT2:p.Gly203Asp	insufficient	0	0
CYLD	CYLD:p.Gly596Asp	insufficient	0	0
CHD9	CHD9:p.Arg1481Trp	insufficient	0	0
ADGRG5	ADGRG5:p.Ala318Val	insufficient	0	0
CES3	CES3:p.Ala90Val	insufficient	0	0
SLC43A2	SLC43A2:p.Val380Ile	insufficient	0	0
KIF1C	KIF1C:p.Glu456Lys	insufficient	0	0
PLSCR3	PLSCR3:p.Gly287Ser	insufficient	0	0
CHRNB1	CHRNB1:p.His340Pro	insufficient	0	0
STX8	STX8:p.Pro234Ser	insufficient	0	0
ULK2	ULK2:p.Val22Leu	insufficient	0	0
JUP	JUP:p.Ala617Val	insufficient	0	0
COASY	COASY:p.Gly44Asp	insufficient	0	0
HDAC5	HDAC5:p.Arg266Cys	insufficient	0	0
SLC25A39	SLC25A39:p.Arg186Trp	insufficient	0	0
TANC2	TANC2:p.Arg1015Trp	insufficient	0	0
CD300H	CD300H:p.Ser157Asn	insufficient	0	0
MYO15B	MYO15B:p.Pro633His	insufficient	0	0
FASN	FASN:p.Gly8Asp	insufficient	0	0
ARHGAP28	ARHGAP28:p.Ala235Val	insufficient	1	0
EPG5	EPG5:p.Ala869Thr	insufficient	0	0
LOXHD1	LOXHD1:p.Ala1280Thr	insufficient	0	0
ATP9B	ATP9B:p.Arg407His	insufficient	0	0
CTDP1	CTDP1:p.Gly476Cys	insufficient	0	0
MED16	MED16:p.Val318Met	insufficient	0	0
SF3A2	SF3A2:p.Gly399Glu	insufficient	1	0
NDUFA11	NDUFA11:p.Arg104Cys	not_expressed	2	0
NACC1	NACC1:p.Thr373Ile	insufficient	0	0
HSH2D	HSH2D:p.Ala316Ser	insufficient	0	0
C19orf44	C19orf44:p.Ala649Val	insufficient	0	0
URI1	URI1:p.Asp153Asn	insufficient	0	0
PEPD	PEPD:p.Gly50Ser	insufficient	1	0
ETV2	ETV2:p.Gly264Asp	insufficient	0	0
POLR2I	POLR2I:p.Ala48Val	not_expressed	2	0
MAP4K1	MAP4K1:p.Gly517Arg	insufficient	0	0
PAK4	PAK4:p.Gly477Asp	insufficient	0	0
MAP3K10	MAP3K10:p.Arg649Trp	insufficient	0	0
TGFB1	TGFB1:p.Arg372His	insufficient	1	0
RPS19	RPS19:p.Val30Ala	not_expressed	3	0
PRKD2	PRKD2:p.Arg192His	insufficient	0	0
BICRA	BICRA:p.Arg1392Cys	insufficient	0	0
RASIP1	RASIP1:p.Ala78Val	insufficient	0	0
LIN7B	LIN7B:p.Pro175Leu	insufficient	0	0
SPACA6	SPACA6:p.Ser279Arg	insufficient	0	0
LENG8	LENG8:p.Ala213Thr	insufficient	0	0
ZNF606	ZNF606:p.Gly305Ser	insufficient	0	0
SIRPA	SIRPA:p.Ala454Val	insufficient	0	0
CDC25B	CDC25B:p.Lys192Thr	insufficient	0	0
SMOX	SMOX:p.Gly249Asp	insufficient	0	0
XRN2	XRN2:p.Gly375Trp	insufficient	0	0
NOL4L	NOL4L:p.Arg270Trp	insufficient	0	0
CSTF1	CSTF1:p.Ala142Thr	insufficient	0	0
HELZ2	HELZ2:p.Ala1802Val	insufficient	0	0
ITSN1	ITSN1:p.Glu1443Gly	insufficient	0	0
BAIAP2L2	BAIAP2L2:p.Gly506Asp	insufficient	0	0
TBC1D22A	TBC1D22A:p.Ala98Thr	insufficient	1	0
WWC3	WWC3:p.Tyr240Asn	insufficient	0	0
MAGEB1	MAGEB1:p.Ala290Val	insufficient	0	0
SHROOM4	SHROOM4:p.Ala1419Val	insufficient	0	0
VSIG4	VSIG4:p.Ile203Val	insufficient	0	0
IGBP1	IGBP1:p.Ile203Thr	insufficient	0	0
ABCB7	ABCB7:p.Gly388Ser	insufficient	0	0
WDR44	WDR44:p.Ala204Val	insufficient	0	0
SLC25A43	SLC25A43:p.Ser83Arg	not_expressed	2	0
NKRF	NKRF:p.Val221Ile	insufficient	0	0
PHF6	PHF6:p.Arg347Gln	insufficient	0	0
CCNQ	CCNQ:p.Gly81Asp	insufficient	0	0
USP9Y	USP9Y:p.Ala2187Val	insufficient	0	0
RAP1GAP	RAP1GAP:p.Arg88His	N/A
CSMD2	CSMD2:p.Arg1116His	N/A
LRRC7	LRRC7:p.Val599Ile	N/A
LCE1B	LCE1B:p.Pro14Ser	N/A
PGLYRP4	PGLYRP4:p.Val288_Gly294del	N/A
DCST2	DCST2:p.Val9Leu	N/A
CHIT1	CHIT1:p.Gly60Asp	N/A
CNTN2	CNTN2:p.Gly965Asp	N/A
OBSCN	OBSCN:p.Pro7410Ser	N/A
KIF26B	KIF26B:p.Ala1734Asp	N/A
C2orf50	C2orf50:p.Arg85His	N/A
NTSR2	NTSR2:p.Arg287Cys	N/A
GPR148	GPR148:p.Leu203Pro	N/A
PPP1R1C	PPP1R1C:p.Ala12Val	N/A
MAP2	MAP2:p.Gly868AlafsTer38	N/A
CELSR3	CELSR3:p.Ala1792Thr	N/A
ERC2	ERC2:p.Lys866Asn	N/A
CNTN3	CNTN3:p.Glu452Asp	N/A
SI	SI:p.Thr587Ile	N/A
ZAR1	ZAR1:p.Ala233Val	N/A
DSPP	DSPP:p.Ser1223_Ser1261del	N/A
SLC9A3	SLC9A3:p.Ala50Val	N/A
H1-2	H1-2:p.Ala197_Lys201del	N/A
PRSS16	PRSS16:p.Ala55Asp	N/A
CCN6	CCN6:p.Leu246Met	N/A
FNDC1	FNDC1:p.Ala91Val	N/A
SP8	SP8:p.Ala148Val	N/A
HOXA13	HOXA13:p.Ala214Thr	N/A
TECPR1	TECPR1:p.Thr259HisfsTer77	N/A
VGF	VGF:p.Pro42Ser	N/A
RP1L1	RP1L1:p.Leu792Val	N/A
CNTNAP3	CNTNAP3:p.Ala1204Thr	N/A
HMCN2	HMCN2:p.Pro3777His	N/A
GTF3C5	GTF3C5:p.Glu496_Glu499del	N/A
DBH	DBH:p.His457Tyr	N/A
GPR158	GPR158:p.Ala106Val	N/A
RET	RET:p.Glu208Lys	N/A
GPRIN2	GPRIN2:p.Arg242Lys	N/A
C10orf71	C10orf71:p.Pro199Ser	N/A
DNTT	DNTT:p.Ala463Val	N/A
PITX3	PITX3:p.Gly224ArgfsTer38	N/A
C10orf120	C10orf120:p.Asp222Val	N/A
HMX2	HMX2:p.Ala145Thr	N/A
CTBP2	CTBP2:p.Pro424Ser	N/A
CFAP46	CFAP46:p.Ala2297Val	N/A
KRTAP5-4	KRTAP5-4:p.Gly34Ser	N/A
OR51S1	OR51S1:p.Pro61Ser	N/A
OR10AG1	OR10AG1:p.Leu256Ile	N/A
CCDC83	CCDC83:p.Pro16Gln	N/A
MUC19	MUC19:p.Ile626Asn	N/A
AMIGO2	AMIGO2:p.Trp243GlyfsTer9	N/A
TSPAN19	TSPAN19:p.Gly74Ser	N/A
PCDH8	PCDH8:p.Leu871Ile	N/A
NALCN	NALCN:p.Phe351Ser	N/A
CCDC168	CCDC168:p.Ser442Ile	N/A
SOX1	SOX1:p.Ala378Val	N/A
GRK1	GRK1:p.Ala510Val	N/A
ESR2	ESR2:p.Pro277Ser	N/A
SLC25A47	SLC25A47:p.Ala119Thr	N/A
AHNAK2	AHNAK2:p.Val2219Met	N/A
AGBL1	AGBL1:p.Leu29Pro	N/A
CASKIN1	CASKIN1:p.Gly905Asp	N/A
C16orf90	C16orf90:p.Gly26Val	N/A
HS3ST4	HS3ST4:p.Pro422Gln	N/A
IRX6	IRX6:p.Ala119Thr	N/A
PITPNM3	PITPNM3:p.Ala638Thr	N/A
NOS2	NOS2:p.Tyr491Ser	N/A
CACNG5	CACNG5:p.Ala183Thr	N/A
MYO15B	MYO15B:p.Pro634ArgfsTer43	N/A
TSPAN10	TSPAN10:p.Ala267Val	N/A
SERPINB11	SERPINB11:p.Ser40Gly	N/A
MUC16	MUC16:p.Gly12343Ser	N/A
OR7D4	OR7D4:p.Lys298Glu	N/A
DMKN	DMKN:p.Gly284Ser	N/A
CCDC8	CCDC8:p.Glu351Gln	N/A
SLC8A2	SLC8A2:p.Ala33Thr	N/A
SHANK1	SHANK1:p.Glu11Lys	N/A
SPEF1	SPEF1:p.Gln230Lys	N/A
DLGAP4	DLGAP4:p.Ala182Thr	N/A
KRTAP10-4	KRTAP10-4:p.Arg62Leu	N/A
KRTAP10-6	KRTAP10-6:p.Arg62Leu	N/A
FTCD	FTCD:p.Ala411Val	N/A
TMPRSS6	TMPRSS6:p.Pro387Ser	N/A
CACNA1I	CACNA1I:p.Cys1163Phe	N/A
MOV10L1	MOV10L1:p.Ser1024Arg	N/A
WWC3	WWC3:p.Gln239HisfsTer33	N/A
FRMPD3	FRMPD3:p.Arg811His	N/A
PASD1	PASD1:p.Asn22Lys	N/A

Per-subclone mutant-allele RNA fraction (AF)

Top neoantigens × subclones.

Units: mutant-allele read fraction (AD ÷ DP), 0–1

Per-subclone source-gene expression

Top neoantigens × subclones.

Units: mean log-normalized expression — ln(1 + counts-per-10k) averaged over the subclone's cells (not raw counts/TPM)

10.50

	S0	S1	S2
ZNF436	1.00	·	·
EXOC4	0.26	0.30	1.00
DYNC1H1	0.67	0.33	·
ZNF880	0.33	·	·
HLA-B	0.15	0.10	0.00
EZR	0.05	0.00	0.00
MORN1	·	0.00	·
UBR4	0.00	·	·
SNRNP40	0.00	·	·
GRIK3	·	0.00	·
WLS	0.00	0.00	·
SYDE2	0.00	0.00	·
CTTNBP2NL	·	0.00	·
TARS2	0.00	·	·
PRRC2C	0.00	0.00	·
PRRC2C	0.00	0.00	·
NCOA1	·	0.00	·
PCBP1	·	0.00	·
MRPS5	·	0.00	0.00
TMEM131	0.00	·	·
FAM168B	0.00	0.00	0.00
UBXN4	0.00	0.00	·
RIF1	·	0.00	·
PLA2R1	0.00	·	·
CCDC150	·	0.00	·
SPATS2L	0.00	·	·
ANKZF1	0.00	0.00	·
IL17RC	·	0.00	·
MSL2	0.00	·	·
HLTF	0.00	·	·

	S0	S1	S2
ZNF436	0.03	0.04	0.00
EXOC4	2.29	1.81	1.94
DYNC1H1	1.26	1.30	0.76
ZNF880	0.09	0.15	0.14
HLA-B	0.40	0.86	0.39
EZR	0.52	0.71	0.32
MORN1	0.06	0.09	0.03
UBR4	0.49	0.32	0.50
SNRNP40	0.18	0.17	0.06
GRIK3	0.00	0.01	0.00
WLS	0.94	0.85	0.62
SYDE2	0.34	0.40	0.27
CTTNBP2NL	0.17	0.20	0.13
TARS2	0.17	0.16	0.11
PRRC2C	1.25	1.29	1.13
PRRC2C	1.25	1.29	1.13
NCOA1	1.06	0.80	0.71
PCBP1	0.23	0.45	0.12
MRPS5	0.30	0.41	0.17
TMEM131	1.25	1.20	0.94
FAM168B	0.35	0.31	0.39
UBXN4	0.50	0.58	0.39
RIF1	0.64	0.59	0.52
PLA2R1	0.52	0.30	0.32
CCDC150	0.12	0.09	0.10
SPATS2L	0.59	0.56	0.30
ANKZF1	0.08	0.14	0.02
IL17RC	0.15	0.19	0.04
MSL2	0.50	0.32	0.47
HLTF	0.29	0.32	0.21

2.31.10

Per-subclone HLA allele-loss screen

Allele-specific HLA loss per subclone (scHLAcount): each subclone × HLA allele, with the allele's share of its gene's reads vs the immune-cell baseline. A flagged allele is the depleted haplotype of an imbalanced gene.

Subclone	Gene	Allele	Allele frac	Immune baseline	Δ vs baseline	Gene depth	Lost
11q-loss	B	B*08:01:02	0.42	0.51	-0.09	109	No
11q-loss	B	B*27:05:03	0.58	0.49	+0.09	109	No
11q-loss	C	C*01:02:02	0.56	0.68	-0.12	110	No
11q-loss	C	C*07:01:04	0.44	0.32	+0.12	110	No
S1	B	B*08:01:02	0.50	0.51	-0.01	223	No
S1	B	B*27:05:03	0.50	0.49	+0.01	223	No
S1	C	C*01:02:02	0.55	0.68	-0.13	233	No
S1	C	C*07:01:04	0.45	0.32	+0.13	233	No
S2	B	B*08:01:02	0.55	0.51	+0.03	11	No
S2	B	B*27:05:03	0.45	0.49	-0.03	11	No
S2	C	C*01:02:02	0.44	0.68	-0.24	9	No
S2	C	C*07:01:04	0.56	0.32	+0.24	9	No

Subclonal Analysis

Single-cell RNA subclone structure of the tumor and which neoantigens are expressed in each subclone.

Clonal lineage tree (CNV based)

Copy-number variation (CNV) — where tumor cells gain or lose whole chunks of chromosomes — is used here to group the tumor's subclones into a lineage, rooted at the normal (diploid) genome. Each subclone is named by its most distinctive chromosome-arm change (e.g. ‘11q-loss’ = loss of chromosome 11's q-arm); the trunk carries changes shared by every subclone. Hover any node for its lesions, cell fraction and neoantigen count.

Subclone cells and neoantigen detection

The same whole-sample UMAP embedding, zoomed to the 211 malignant cells. Shape identifies the subclone; color shows detected mutant RNA.

Each marker represents one malignant cell; shape identifies its subclone. Yellow indicates detection of at least one RNA read carrying EXOC4:p.Ser34Ile, and red indicates DYNC1H1:p.Val314Ile. No cells have both mutant RNAs detected. Hollow markers identify 162 cells with no coverage at either mutation site. Filled gray markers identify 30 cells with coverage but no detected mutant reads: 26 have coverage at EXOC4 only, three at DYNC1H1 only, and one at both. Coverage here means at least one read. Hover a cell for its subclone and mutant/total read counts at each site.

Neoantigen presence by subclone (RNA-expressed)

Each candidate's mutant-allele RNA fraction (AF) within each subclone — deeper green = higher AF.

34 candidate(s) covered in ≥1 subclone; 260 with no single-cell coverage are omitted.

#	Gene	Variant	Clonality	11q-loss	S1	S2	expr / cov
1	EXOC4	EXOC4:p.Ser34Ile	clonal	0.26	0.30	1.00	2 / 2
2	DYNC1H1	DYNC1H1:p.Val314Ile	clonal	0.67	0.33	·	2 / 2
3	HLA-B	HLA-B:p.Glu100Val	subclonal	0.15	0.10	0	2 / 3
4	EZR	EZR:p.Pro2Ser	subclonal	0.05	0	0	1 / 2
5	SYDE2	SYDE2:p.Gly141Val	not_expressed	0	0	·	0 / 2
6	FAM168B	FAM168B:p.Ala31Val	not_expressed	0	0	0	0 / 2
7	TMEM44	TMEM44:p.Leu50Arg	not_expressed	0	0	0	0 / 2
8	C6orf62	C6orf62:p.Pro57Ser	not_expressed	0	0	·	0 / 2
9	LAMA4	LAMA4:p.Gly1688Asp	not_expressed	0	0	·	0 / 2
10	ITGB1	ITGB1:p.Gly550Asp	not_expressed	0	0	0	0 / 2
11	VSTM4	VSTM4:p.Ala94Thr	not_expressed	0	0	·	0 / 2
12	MCMBP	MCMBP:p.Gly17Glu	not_expressed	0	0	·	0 / 2
13	NDUFA11	NDUFA11:p.Arg104Cys	not_expressed	0	0	0	0 / 2
14	POLR2I	POLR2I:p.Ala48Val	not_expressed	0	0	·	0 / 2
15	RPS19	RPS19:p.Val30Ala	not_expressed	0	0	0	0 / 3
16	SLC25A43	SLC25A43:p.Ser83Arg	not_expressed	0	0	·	0 / 2
17	ZNF880	ZNF880:p.Cys413Phe	insufficient	0.33	·	·	1 / 1
18	WLS	WLS:p.Trp460Arg	insufficient	0	0	·	0 / 1
19	PRRC2C	PRRC2C:p.Ala2147Val	insufficient	0	0	·	0 / 1
20	PRRC2C	PRRC2C:p.Thr2152Ile	insufficient	0	0	·	0 / 1
21	TMEM131	TMEM131:p.Ser224Asn	insufficient	0	·	·	0 / 1
22	LRBA	LRBA:p.Ala49Val	insufficient	0	0	·	0 / 1
23	TMEM131L	TMEM131L:p.Ala16Thr	insufficient	0	0	·	0 / 1
24	PHF3	PHF3:p.Arg971Trp	insufficient	0	0	·	0 / 1
25	OTUD6B	OTUD6B:p.Thr6Ser	insufficient	0	0	·	0 / 1
26	TMBIM4	TMBIM4:p.Arg230Gln	insufficient	0	0	0	0 / 1
27	PARP4	PARP4:p.Ala373Thr	insufficient	0	·	·	0 / 1
28	LTBP2	LTBP2:p.Gly1088Asp	insufficient	·	0	·	0 / 1
29	MCRIP2	MCRIP2:p.Glu30Lys	insufficient	0	0	0	0 / 1
30	ARHGAP28	ARHGAP28:p.Ala235Val	insufficient	0	0	·	0 / 1
31	SF3A2	SF3A2:p.Gly399Glu	insufficient	0	0	·	0 / 1
32	PEPD	PEPD:p.Gly50Ser	insufficient	0	0	0	0 / 1
33	TGFB1	TGFB1:p.Arg372His	insufficient	0	0	0	0 / 1
34	TBC1D22A	TBC1D22A:p.Ala98Thr	insufficient	0	0	0	0 / 1

mutant expressed (AF, deeper = higher)covered, mutant absentno single-cell coverage

Neoantigen prioritization

Ranked neoantigen vaccine targets, from the Tier1 shortlist to the full tiered list.

The shortlist (Tier1 targets)

The shortlist: neoantigens that are immunogenic AND expressed in tumor cells AND clonal.

Gene	Mutation	Type	MHC class	CD8 prob	CD4 prob	Tumor-cell AF	Tumor-cell depth	Clonality	Subclones expressed	Subclones covered
DYNC1H1	DYNC1H1:p.Val314Ile	missense	I+II	0.80	0.61	0.44	9	clonal	2	2
EXOC4	EXOC4:p.Ser34Ile	missense	I+II	0.47	0.59	0.29	52	clonal	2	2

Full ranked candidate table

The full ranked table of every candidate, each assigned a tier (Tier1 → Tier2 → Tier3 → deprioritized_silent → deprioritized_no_expr → not_immunogenic).

Gene	Mutation	Type	MHC class	CD8 prob	CD4 prob	Tumor-cell AF	Expressed	Clonal	Tier
DYNC1H1	DYNC1H1:p.Val314Ile	missense	I+II	0.80	0.61	0.44	Yes	Yes	1
EXOC4	EXOC4:p.Ser34Ile	missense	I+II	0.47	0.59	0.29	Yes	Yes	1
ZNF436	ZNF436:p.Ser207Cys	missense	I	0.51	0.37	1.00	Yes	No	2
MAP2	MAP2:p.Gly868AlafsTer38	frameshift	I+II	0.89	0.61		No	No	3
TECPR1	TECPR1:p.Thr259HisfsTer77	frameshift	I+II	0.78	0.83		No	No	3
CHRNB1	CHRNB1:p.His340Pro	missense	I	0.79	0.13		No	No	3
MORN1	MORN1:p.Cys196Tyr	missense	I	0.77	0.39	0.00	No	No	3
SMOX	SMOX:p.Gly249Asp	missense	I+II	0.59	0.77	0.00	No	No	3
TTBK2	TTBK2:p.Pro593Arg	missense	I+II	0.75	0.55		No	No	3
LRRFIP2	LRRFIP2:p.Arg345Gln	splice	I+II	0.53	0.75		No	No	3
MYO15B	MYO15B:p.Pro634ArgfsTer43	frameshift	I+II	0.75	0.46		No	No	3
ZNF606	ZNF606:p.Gly305Ser	missense	I+II	0.43	0.73		No	No	3
PITX3	PITX3:p.Gly224ArgfsTer38	frameshift	I	0.71	0.27		No	No	3
SNRNP40	SNRNP40:p.Arg260Ser	splice	I+II	0.49	0.69	0.00	No	No	3
MSL2	MSL2:p.Ala514Val	missense	I+II	0.45	0.69	0.00	No	No	3
NCOA1	NCOA1:p.Ala310Val	missense	I+II	0.60	0.69	0.00	No	No	3
MAP2	MAP2:p.Leu867Met	missense	I+II	0.68	0.56		No	No	3
WDR44	WDR44:p.Ala204Val	missense	II	0.34	0.68	0.00	No	No	3
FHL3	FHL3:p.Pro143Ser	missense	I+II	0.68	0.57		No	No	3
SLC9A3	SLC9A3:p.Ala50Val	missense	II	0.32	0.67		No	No	3
NBPF3	NBPF3:p.Phe429Cys	missense	I	0.67	0.38		No	No	3
SCAF8	SCAF8:p.Pro694Ser	missense	I	0.67	0.15		No	No	3
SYNE1	SYNE1:p.Ala4264Val	missense	II	0.36	0.67		No	No	3
PCDH8	PCDH8:p.Leu871Ile	missense	I+II	0.41	0.66		No	No	3
NOS2	NOS2:p.Tyr491Ser	missense	I+II	0.55	0.66		No	No	3
CYLD	CYLD:p.Gly596Asp	missense	I+II	0.65	0.41	0.00	No	No	3
IL17RC	IL17RC:p.Ala587Val	missense	I+II	0.65	0.49	0.00	No	No	3
SPTBN5	SPTBN5:p.Ala1719Val	missense	I+II	0.44	0.65		No	No	3
FRMPD3	FRMPD3:p.Arg811His	missense	I+II	0.43	0.65		No	No	3
CHIT1	CHIT1:p.Gly60Asp	missense	I	0.65	0.29		No	No	3
CASKIN1	CASKIN1:p.Gly905Asp	missense	I+II	0.49	0.65		No	No	3
FJX1	FJX1:p.Ter438TrpextTer80	stop_lost	I+II	0.64	0.61		No	No	3
MAP2	MAP2:p.Leu867Arg	missense	I+II	0.64	0.55		No	No	3
RIOK1	RIOK1:p.Glu250Lys	missense	I+II	0.51	0.64		No	No	3
RAP1GAP	RAP1GAP:p.Arg88His	missense	I	0.64	0.27		No	No	3
NUP188	NUP188:p.Ala1087Thr	missense	II	0.33	0.64	0.00	No	No	3
PITPNM3	PITPNM3:p.Ala638Thr	missense	II	0.39	0.64		No	No	3
GNPTAB	GNPTAB:p.Ala1122Ser	missense	I+II	0.42	0.63		No	No	3
CFAP46	CFAP46:p.Ala2297Val	missense	II	0.38	0.63		No	No	3
FGL2	FGL2:p.Asp212Tyr	missense	I+II	0.54	0.62		No	No	3
ETV2	ETV2:p.Gly264Asp	missense	I	0.62	0.12		No	No	3
FNDC1	FNDC1:p.Ala91Val	missense	I+II	0.48	0.62		No	No	3
MAP3K10	MAP3K10:p.Arg649Trp	missense	II	0.31	0.62		No	No	3
PPP1R1C	PPP1R1C:p.Ala12Val	missense	I+II	0.62	0.56		No	No	3
UBR4	UBR4:p.Arg1628Gln	missense	I+II	0.42	0.61		No	No	3
DNTT	DNTT:p.Ala463Val	missense	I+II	0.61	0.55		No	No	3
KIF26B	KIF26B:p.Ala1734Asp	missense	I+II	0.60	0.46		No	No	3
PLA2R1	PLA2R1:p.Trp519Leu	missense	I	0.60	0.14	0.00	No	No	3
VPS37C	VPS37C:p.Pro267Ser	missense	I	0.60	0.36	0.00	No	No	3
IRX6	IRX6:p.Ala119Thr	missense	I+II	0.60	0.42		No	No	3
RIPK2	RIPK2:p.Asp211Asn	missense	I+II	0.59	0.51		No	No	3
IFT122	IFT122:p.Arg798His	missense	I+II	0.51	0.59		No	No	3
HLTF	HLTF:p.Pro239Leu	missense	I+II	0.49	0.59	0.00	No	No	3
CDC40	CDC40:p.Val507Ile	missense	II	0.34	0.59		No	No	3
CCNQ	CCNQ:p.Gly81Asp	missense	I+II	0.53	0.59	0.00	No	No	3
H1-2	H1-2:p.Ala197_Lys201del	inframe_del	I+II	0.42	0.59		No	No	3
COASY	COASY:p.Gly44Asp	missense	I+II	0.43	0.59	0.00	No	No	3
TANC2	TANC2:p.Arg1015Trp	missense	I+II	0.59	0.43		No	No	3
SLC25A47	SLC25A47:p.Ala119Thr	missense	I+II	0.46	0.58		No	No	3
VWF	VWF:p.Glu954Gly	missense	I+II	0.44	0.58		No	No	3
TGFBR3	TGFBR3:p.Cys572Tyr	missense	I+II	0.58	0.52		No	No	3
ADAMTS2	ADAMTS2:p.Asp650Asn	missense	I+II	0.58	0.55	0.00	No	No	3
AHNAK2	AHNAK2:p.Val2219Met	missense	II	0.30	0.58		No	No	3
CUL9	CUL9:p.Asp394Tyr	missense	I+II	0.58	0.58		No	No	3
C16orf90	C16orf90:p.Gly26Val	missense	I+II	0.50	0.58		No	No	3
DBH	DBH:p.His457Tyr	missense	I+II	0.51	0.58		No	No	3
LRRC7	LRRC7:p.Val599Ile	splice	I+II	0.58	0.42		No	No	3
FUCA1	FUCA1:p.Arg178Cys	missense	I	0.57	0.30		No	No	3
HERC3	HERC3:p.Glu382Lys	splice	I+II	0.48	0.57	0.00	No	No	3
MYO9A	MYO9A:p.Asp523Val	missense	I+II	0.57	0.49		No	No	3
ZFYVE1	ZFYVE1:p.Ala503Val	missense	II	0.34	0.57		No	No	3
KDM3B	KDM3B:p.Pro633Ser	missense	I+II	0.54	0.57	0.00	No	No	3
OPLAH	OPLAH:p.Pro841Ser	missense	I+II	0.50	0.57		No	No	3
ARHGAP1	ARHGAP1:p.Ala285Thr	missense	I+II	0.50	0.57		No	No	3
ATP7B	ATP7B:p.Ala1063Val	missense	II	0.30	0.57	0.00	No	No	3
LIN7B	LIN7B:p.Pro175Leu	missense	I+II	0.52	0.57	0.00	No	No	3
CSMD2	CSMD2:p.Arg1116His	missense	I	0.57	0.17		No	No	3
CD200R1	CD200R1:p.Pro258Leu	missense	I+II	0.52	0.56		No	No	3
CACNA1I	CACNA1I:p.Cys1163Phe	missense	I+II	0.50	0.56		No	No	3
HMCN2	HMCN2:p.Pro3777His	missense	I+II	0.48	0.56		No	No	3
IGBP1	IGBP1:p.Ile203Thr	missense	I+II	0.43	0.56	0.00	No	No	3
GPR158	GPR158:p.Ala106Val	missense	I+II	0.56	0.51		No	No	3
CCDC150	CCDC150:p.Arg589His	missense	I+II	0.55	0.56	0.00	No	No	3
CSTF1	CSTF1:p.Ala142Thr	missense	I+II	0.45	0.56		No	No	3
PHF6	PHF6:p.Arg347Gln	missense	II	0.32	0.56		No	No	3
CCDC8	CCDC8:p.Glu351Gln	missense	II	0.28	0.55		No	No	3
TARS2	TARS2:p.Ala439Thr	missense	I+II	0.43	0.55	0.00	No	No	3
NKRF	NKRF:p.Val221Ile	missense	I+II	0.43	0.55	0.00	No	No	3
CCDC168	CCDC168:p.Ser442Ile	missense	I+II	0.55	0.55		No	No	3
ANLN	ANLN:p.Ser553Cys	missense	II	0.34	0.55		No	No	3
RET	RET:p.Glu208Lys	missense	I+II	0.55	0.42		No	No	3
HOXA13	HOXA13:p.Ala214Thr	missense	II	0.40	0.55		No	No	3
RP1L1	RP1L1:p.Leu792Val	missense	II	0.22	0.55		No	No	3
SIRPA	SIRPA:p.Ala454Val	missense	I+II	0.41	0.55		No	No	3
SCRIB	SCRIB:p.Ala1461Thr	missense	I+II	0.40	0.55		No	No	3
ERC2	ERC2:p.Lys866Asn	missense	II	0.32	0.55		No	No	3
ULK2	ULK2:p.Val22Leu	missense	II	0.31	0.55		No	No	3
SPEF1	SPEF1:p.Gln230Lys	missense	I	0.55	0.38		No	No	3
CARS2	CARS2:p.Ala235Thr	missense	II	0.40	0.55		No	No	3
CYP1B1	CYP1B1:p.Arg43Trp	missense	I	0.55	0.36		No	No	3
DCST2	DCST2:p.Val9Leu	missense	I	0.55	0.38		No	No	3
NUP210	NUP210:p.Ala1857Thr	missense	I+II	0.49	0.55		No	No	3
PRKD2	PRKD2:p.Arg192His	missense	I+II	0.40	0.54		No	No	3
CTTNBP2NL	CTTNBP2NL:p.Arg96His	missense	I+II	0.42	0.54	0.00	No	No	3
UBR4	UBR4:p.Ala4907Val	missense	I+II	0.45	0.54	0.00	No	No	3
RNF40	RNF40:p.Gly436Glu	missense	I+II	0.49	0.54	0.00	No	No	3
VGF	VGF:p.Pro42Ser	missense	I+II	0.41	0.54		No	No	3
CNTN2	CNTN2:p.Gly965Asp	missense	I+II	0.48	0.54		No	No	3
SMARCAL1	SMARCAL1:p.Gly463Arg	missense	I+II	0.47	0.53		No	No	3
HSH2D	HSH2D:p.Ala316Ser	missense	I+II	0.42	0.53		No	No	3
BACE1	BACE1:p.Arg408Trp	missense	I+II	0.53	0.53	0.00	No	No	3
ADGRF5	ADGRF5:p.Asn1279Ser	missense	I+II	0.53	0.51		No	No	3
WWC3	WWC3:p.Gln239HisfsTer33	frameshift	I+II	0.53	0.49		No	No	3
CFAP58	CFAP58:p.Ala478Thr	missense	I+II	0.43	0.53		No	No	3
PAK4	PAK4:p.Gly477Asp	missense	I+II	0.53	0.48	0.00	No	No	3
SLC33A1	SLC33A1:p.Ala131Val	missense	I+II	0.41	0.53	0.00	No	No	3
LYST	LYST:p.Gly1812Asp	missense	I	0.53	0.40		No	No	3
PC	PC:p.Gly150Glu	missense	II	0.30	0.53		No	No	3
VPS13B	VPS13B:p.Ser3731Phe	missense	I	0.53	0.16		No	No	3
RASIP1	RASIP1:p.Ala78Val	missense	I	0.52	0.39	0.00	No	No	3
MED16	MED16:p.Val318Met	missense	II	0.39	0.52		No	No	3
HFM1	HFM1:p.Ala1062Val	missense	II	0.39	0.52		No	No	3
CCN6	CCN6:p.Leu246Met	missense	I	0.52	0.12		No	No	3
CNTN3	CNTN3:p.Glu452Asp	missense	I+II	0.45	0.52		No	No	3
SLC25A39	SLC25A39:p.Arg186Trp	missense	I+II	0.48	0.52	0.00	No	No	3
LNP1	LNP1:p.His65Leu	missense	I	0.52	0.14		No	No	3
MOV10L1	MOV10L1:p.Ser1024Arg	missense	II	0.38	0.52		No	No	3
VSIG4	VSIG4:p.Ile203Val	missense	I+II	0.51	0.52		No	No	3
LRATD1	LRATD1:p.Ala172Thr	missense	II	0.30	0.52		No	No	3
ANKRD33B	ANKRD33B:p.Gly364Ser	missense	II	0.05	0.51		No	No	3
ZC3H12C	ZC3H12C:p.Glu434Lys	missense	I+II	0.46	0.51		No	No	3
ESR2	ESR2:p.Pro277Ser	missense	II	0.40	0.51		No	No	3
ATP1A1	ATP1A1:p.Glu544Lys	missense	I+II	0.51	0.41		No	No	3
MYO15B	MYO15B:p.Pro633His	missense	I+II	0.41	0.51		No	No	3
RAB11FIP3	RAB11FIP3:p.Ala101Val	missense	I+II	0.43	0.51		No	No	3
PHGDH	PHGDH:p.Ala255Val	missense	II	0.30	0.50		No	No	3
MAP4K1	MAP4K1:p.Gly517Arg	missense	I+II	0.50	0.50	0.00	No	No	3
HPS1	HPS1:p.Phe301Val	missense	II	0.32	0.50		No	No	3
LENG8	LENG8:p.Ala213Thr	missense	I	0.50	0.30	0.00	No	No	3
HS3ST4	HS3ST4:p.Pro422Gln	missense	II	0.39	0.50		No	No	3
EHD3	EHD3:p.Asn295His	missense	I	0.50	0.27		No	No	3
SLC25A12	SLC25A12:p.Ile347Thr	missense	I+II	0.50	0.41		No	No	3
CHD9	CHD9:p.Arg1481Trp	missense	I	0.50	0.27		No	No	3
CDC25B	CDC25B:p.Lys192Thr	missense	I	0.50	0.31		No	No	3
CDC42BPG	CDC42BPG:p.Ala792Thr	missense	I+II	0.41	0.50		No	No	3
ROBO2	ROBO2:p.Asn1068Lys	missense	II	0.33	0.49		No	No	3
DNHD1	DNHD1:p.Arg1551Trp	missense	II	0.24	0.49	0.00	No	No	3
BRAP	BRAP:p.Arg534His	missense	I+II	0.48	0.49		No	No	3
KIF1C	KIF1C:p.Glu456Lys	missense	II	0.34	0.49		No	No	3
TMPRSS6	TMPRSS6:p.Pro387Ser	missense	I+II	0.40	0.49		No	No	3
BLTP3B	BLTP3B:p.Ala473Val	missense	II	0.34	0.49	0.00	No	No	3
HELZ2	HELZ2:p.Ala1802Val	missense	I	0.49	0.29		No	No	3
AHDC1	AHDC1:p.Arg832His	missense	I+II	0.48	0.42		No	No	3
HDAC5	HDAC5:p.Arg266Cys	missense	I+II	0.48	0.44	0.00	No	No	3
TGS1	TGS1:p.Ala709Val	missense	II	0.32	0.48	0.00	No	No	3
GPR52	GPR52:p.His109Asp	missense	I	0.48	0.35		No	No	3
CCDC83	CCDC83:p.Pro16Gln	missense	I+II	0.47	0.43		No	No	3
TRIM6	TRIM6:p.Ala103Thr	missense	I	0.46	0.28		No	No	3
EPG5	EPG5:p.Ala869Thr	missense	II	0.39	0.46		No	No	3
SI	SI:p.Thr587Ile	missense	I+II	0.46	0.41		No	No	3
SLC43A2	SLC43A2:p.Val380Ile	missense	I+II	0.46	0.46		No	No	3
IQSEC3	IQSEC3:p.Tyr1156Asn	missense	I	0.46	0.09		No	No	3
SHROOM4	SHROOM4:p.Ala1419Val	missense	II	0.31	0.46		No	No	3
BICRA	BICRA:p.Arg1392Cys	missense	I	0.46	0.12		No	No	3
TSPAN19	TSPAN19:p.Gly74Ser	missense	I	0.45	0.13		No	No	3
ADGRG5	ADGRG5:p.Ala318Val	missense	I	0.45	0.12		No	No	3
KRTAP10-6	KRTAP10-6:p.Arg62Leu	missense	I	0.45	0.05		No	No	3
BTD	BTD:p.Phe423Val	missense	I+II	0.45	0.45		No	No	3
C2orf50	C2orf50:p.Arg85His	missense	II	0.39	0.45		No	No	3
USP9Y	USP9Y:p.Ala2187Val	missense	I	0.45	0.24		No	No	3
PLSCR3	PLSCR3:p.Gly287Ser	missense	II	0.39	0.45	0.00	No	No	3
CRACD	CRACD:p.Ala647Val	missense	I	0.45	0.27	0.00	No	No	3
CNTNAP3	CNTNAP3:p.Ala1204Thr	missense	II	0.39	0.44		No	No	3
PRSS16	PRSS16:p.Ala55Asp	missense	I	0.44	0.22		No	No	3
ABCB7	ABCB7:p.Gly388Ser	missense	I	0.44	0.15		No	No	3
GPT2	GPT2:p.Gly203Asp	missense	II	0.24	0.44		No	No	3
OBSCN	OBSCN:p.Pro7410Ser	missense	I	0.43	0.16		No	No	3
NACC1	NACC1:p.Thr373Ile	splice	I	0.43	0.38		No	No	3
DLGAP4	DLGAP4:p.Ala182Thr	missense	I	0.43	0.14		No	No	3
CTBP2	CTBP2:p.Pro424Ser	missense	I	0.42	0.39		No	No	3
MUC19	MUC19:p.Ile626Asn	missense	II	0.23	0.42		No	No	3
UBQLN3	UBQLN3:p.Ser554Asn	missense	II	0.24	0.42	0.00	No	No	3
TRMO	TRMO:p.Gly205Glu	missense	I	0.42	0.13	0.00	No	No	3
EEF2KMT	EEF2KMT:p.Ala231Thr	missense	II	0.39	0.41		No	No	3
KRT18	KRT18:p.Ala287Ser	missense	II	0.30	0.41		No	No	3
MUC16	MUC16:p.Gly12343Ser	missense	I	0.41	0.36		No	No	3
CES3	CES3:p.Ala90Val	missense	I	0.41	0.37	0.00	No	No	3
URI1	URI1:p.Asp153Asn	splice	II	0.34	0.41		No	No	3
TMEM131	TMEM131:p.Ser224Asn	missense	I	0.79	0.40	0.00	No	No	deprioritized_silent
NOL4L	NOL4L:p.Arg270Trp	missense	I+II	0.69	0.61	0.00	No	No	deprioritized_silent
TNS2	TNS2:p.Ala484Val	missense	I+II	0.48	0.69	0.00	No	No	deprioritized_silent
MCMBP	MCMBP:p.Gly17Glu	missense	I+II	0.48	0.68	0.00	No	No	deprioritized_silent
LRBA	LRBA:p.Ala49Val	missense	I+II	0.68	0.51	0.00	No	No	deprioritized_silent
ARHGAP28	ARHGAP28:p.Ala235Val	missense	I+II	0.48	0.68	0.00	No	No	deprioritized_silent
SYDE2	SYDE2:p.Gly141Val	missense	I+II	0.68	0.57	0.00	No	No	deprioritized_silent
ABCF2	ABCF2:p.Asp421Glu	missense	I+II	0.45	0.67	0.00	No	No	deprioritized_silent
SPACA6	SPACA6:p.Ser279Arg	missense	I+II	0.60	0.65	0.00	No	No	deprioritized_silent
ITGB1	ITGB1:p.Gly550Asp	missense	I+II	0.45	0.65	0.00	No	No	deprioritized_silent
WLS	WLS:p.Trp460Arg	missense	I+II	0.64	0.58	0.00	No	No	deprioritized_silent
PEPD	PEPD:p.Gly50Ser	missense	I+II	0.63	0.56	0.00	No	No	deprioritized_silent
PHF3	PHF3:p.Arg971Trp	missense	I+II	0.63	0.57	0.00	No	No	deprioritized_silent
TGFB1	TGFB1:p.Arg372His	missense	I+II	0.55	0.63	0.00	No	No	deprioritized_silent
NGDN	NGDN:p.Ala280Thr	missense	I+II	0.46	0.63	0.00	No	No	deprioritized_silent
XRN2	XRN2:p.Gly375Trp	splice	I+II	0.62	0.44	0.00	No	No	deprioritized_silent
ANKZF1	ANKZF1:p.Ala650Val	missense	I+II	0.61	0.58	0.00	No	No	deprioritized_silent
ATP9B	ATP9B:p.Arg407His	missense	I	0.59	0.21	0.00	No	No	deprioritized_silent
TNIK	TNIK:p.Arg299His	missense	I+II	0.53	0.59	0.00	No	No	deprioritized_silent
WWC3	WWC3:p.Tyr240Asn	missense	I+II	0.47	0.59	0.00	No	No	deprioritized_silent
FXR1	FXR1:p.Gly298Arg	missense	II	0.34	0.59	0.00	No	No	deprioritized_silent
LAMA4	LAMA4:p.Gly1688Asp	missense	I+II	0.48	0.59	0.00	No	No	deprioritized_silent
PRRC2C	PRRC2C:p.Thr2152Ile	missense	I+II	0.58	0.56	0.00	No	No	deprioritized_silent
UBXN4	UBXN4:p.Lys480Met	missense	I+II	0.54	0.58	0.00	No	No	deprioritized_silent
HIP1	HIP1:p.Gly956Asp	missense	II	0.34	0.58	0.00	No	No	deprioritized_silent
XPO5	XPO5:p.Lys704Thr	missense	II	0.25	0.57	0.00	No	No	deprioritized_silent
C6orf62	C6orf62:p.Pro57Ser	missense	I+II	0.48	0.57	0.00	No	No	deprioritized_silent
BAIAP2L2	BAIAP2L2:p.Gly506Asp	splice	I+II	0.42	0.57	0.00	No	No	deprioritized_silent
VSTM4	VSTM4:p.Ala94Thr	missense	I	0.57	0.37	0.00	No	No	deprioritized_silent
FASN	FASN:p.Gly8Asp	missense	I+II	0.46	0.57	0.00	No	No	deprioritized_silent
SEC24D	SEC24D:p.Ala284Val	missense	II	0.36	0.57	0.00	No	No	deprioritized_silent
UBE3A	UBE3A:p.Asp698Asn	missense	I+II	0.44	0.56	0.00	No	No	deprioritized_silent
RBM28	RBM28:p.Ala464Thr	missense	I+II	0.49	0.56	0.00	No	No	deprioritized_silent
OTUD6B	OTUD6B:p.Thr6Ser	missense	II	0.32	0.56	0.00	No	No	deprioritized_silent
MAGEB1	MAGEB1:p.Ala290Val	missense	I+II	0.42	0.55	0.00	No	No	deprioritized_silent
RPS19	RPS19:p.Val30Ala	missense	I+II	0.55	0.48	0.00	No	No	deprioritized_silent
TBC1D22A	TBC1D22A:p.Ala98Thr	missense	I+II	0.44	0.55	0.00	No	No	deprioritized_silent
PRRC2C	PRRC2C:p.Ala2147Val	missense	I+II	0.44	0.55	0.00	No	No	deprioritized_silent
MRPS5	MRPS5:p.Ser386Phe	missense	I+II	0.55	0.53	0.00	No	No	deprioritized_silent
FAM168B	FAM168B:p.Ala31Val	missense	I+II	0.43	0.55	0.00	No	No	deprioritized_silent
SLC25A43	SLC25A43:p.Ser83Arg	missense	I	0.54	0.13	0.00	No	No	deprioritized_silent
JUP	JUP:p.Ala617Val	missense	II	0.15	0.54	0.00	No	No	deprioritized_silent
MCU	MCU:p.Leu9Val	missense	I	0.51	0.29	0.00	No	No	deprioritized_silent
PARP4	PARP4:p.Ala373Thr	missense	I	0.51	0.37	0.00	No	No	deprioritized_silent
C19orf44	C19orf44:p.Ala649Val	missense	I+II	0.43	0.50	0.00	No	No	deprioritized_silent
SF3A2	SF3A2:p.Gly399Glu	missense	I	0.49	0.25	0.00	No	No	deprioritized_silent
PCBP1	PCBP1:p.Arg306His	missense	I+II	0.43	0.49	0.00	No	No	deprioritized_silent
RIF1	RIF1:p.Val1366Ile	missense	I+II	0.46	0.48	0.00	No	No	deprioritized_silent
TMBIM4	TMBIM4:p.Arg230Gln	missense	I	0.48	0.29	0.00	No	No	deprioritized_silent
EZR	EZR:p.Pro2Ser	missense	I+II	0.43	0.48	0.02	No	No	deprioritized_silent
ABCC4	ABCC4:p.Ala859Val	missense	II	0.25	0.47	0.00	No	No	deprioritized_silent
MCRIP2	MCRIP2:p.Glu30Lys	missense	I	0.47	0.13	0.00	No	No	deprioritized_silent
TMEM131L	TMEM131L:p.Ala16Thr	missense	I	0.46	0.07	0.00	No	No	deprioritized_silent
ZNF880	ZNF880:p.Cys413Phe	missense	I+II	0.46	0.43	0.33	No	No	deprioritized_silent
TMEM44	TMEM44:p.Leu50Arg	missense	I+II	0.46	0.40	0.00	No	No	deprioritized_silent
NEO1	NEO1:p.Met855Ile	missense	I	0.46	0.31	0.00	No	No	deprioritized_silent
NDUFA11	NDUFA11:p.Arg104Cys	missense	I	0.46	0.04	0.00	No	No	deprioritized_silent
POLR2I	POLR2I:p.Ala48Val	missense	I	0.45	0.22	0.00	No	No	deprioritized_silent
BCL7A	BCL7A:p.Asp88Asn	missense	I	0.45	0.12	0.00	No	No	deprioritized_silent
PHRF1	PHRF1:p.Pro221Ser	missense	I	0.43	0.31	0.00	No	No	deprioritized_silent
LTBP2	LTBP2:p.Gly1088Asp	missense	II	0.04	0.41	0.00	No	No	deprioritized_silent
OR7D4	OR7D4:p.Lys298Glu	missense	II	0.37	0.62		No	No	deprioritized_no_expr
FTCD	FTCD:p.Ala411Val	missense	I+II	0.57	0.61		No	No	deprioritized_no_expr
AGBL1	AGBL1:p.Leu29Pro	missense	I+II	0.53	0.59		No	No	deprioritized_no_expr
C10orf120	C10orf120:p.Asp222Val	missense	II	0.22	0.58		No	No	deprioritized_no_expr
TSPAN10	TSPAN10:p.Ala267Val	missense	I+II	0.55	0.53		No	No	deprioritized_no_expr
C10orf71	C10orf71:p.Pro199Ser	missense	I+II	0.48	0.55		No	No	deprioritized_no_expr
OR51S1	OR51S1:p.Pro61Ser	missense	I+II	0.55	0.51		No	No	deprioritized_no_expr
SOX1	SOX1:p.Ala378Val	missense	I+II	0.54	0.40		No	No	deprioritized_no_expr
GPR148	GPR148:p.Leu203Pro	missense	I	0.52	0.26		No	No	deprioritized_no_expr
CACNG5	CACNG5:p.Ala183Thr	missense	I+II	0.41	0.52		No	No	deprioritized_no_expr
SP8	SP8:p.Ala148Val	missense	II	0.29	0.51		No	No	deprioritized_no_expr
PASD1	PASD1:p.Asn22Lys	missense	I	0.51	0.37		No	No	deprioritized_no_expr
NTSR2	NTSR2:p.Arg287Cys	missense	I	0.48	0.14		No	No	deprioritized_no_expr
GRK1	GRK1:p.Ala510Val	missense	II	0.30	0.48		No	No	deprioritized_no_expr
KRTAP10-4	KRTAP10-4:p.Arg62Leu	missense	I	0.45	0.05		No	No	deprioritized_no_expr
PGLYRP4	PGLYRP4:p.Val288_Gly294del	inframe_del	I	0.44	0.35		No	No	deprioritized_no_expr
CD300H	CD300H:p.Ser157Asn	missense	I	0.40	0.09		No	No	deprioritized_no_expr
CELSR3	CELSR3:p.Ala1792Thr	missense	none	0.40	0.25		No	No	not_immunogenic
ITSN1	ITSN1:p.Glu1443Gly	missense	none	0.26	0.40		No	No	not_immunogenic
GTF3C5	GTF3C5:p.Glu496_Glu499del	inframe_del	none	0.07	0.40		No	No	not_immunogenic
DSPP	DSPP:p.Ser1223_Ser1261del	inframe_del	none	0.40	0.01		No	No	not_immunogenic
PGAP1	PGAP1:p.Thr691Met	missense	none	0.39	0.11		No	No	not_immunogenic
CLDN10	CLDN10:p.Ala47Thr	missense	none	0.39	0.37		No	No	not_immunogenic
NALCN	NALCN:p.Phe351Ser	missense	none	0.39	0.33		No	No	not_immunogenic
HMX2	HMX2:p.Ala145Thr	missense	none	0.39	0.14		No	No	not_immunogenic
ZAR1	ZAR1:p.Ala233Val	missense	none	0.22	0.39		No	No	not_immunogenic
SERPINB11	SERPINB11:p.Ser40Gly	missense	none	0.38	0.26		No	No	not_immunogenic
CLRN1	CLRN1:p.Val47Ile	missense	none	0.38	0.33		No	No	not_immunogenic
OR10AG1	OR10AG1:p.Leu256Ile	missense	none	0.38	0.15		No	No	not_immunogenic
SPPL2A	SPPL2A:p.Gly282Asp	missense	none	0.36	0.12	0.00	No	No	not_immunogenic
GRIK3	GRIK3:p.Arg801Trp	missense	none	0.23	0.34	0.00	No	No	not_immunogenic
SHANK1	SHANK1:p.Glu11Lys	missense	none	0.31	0.23		No	No	not_immunogenic
AMIGO2	AMIGO2:p.Trp243GlyfsTer9	frameshift	none	0.30	0.01		No	No	not_immunogenic
CTDP1	CTDP1:p.Gly476Cys	missense	none	0.30	0.12		No	No	not_immunogenic
GPRIN2	GPRIN2:p.Arg242Lys	missense	none	0.29	0.09		No	No	not_immunogenic
LOXHD1	LOXHD1:p.Ala1280Thr	missense	none	0.29	0.29		No	No	not_immunogenic
SPATS2L	SPATS2L:p.Ala450Thr	missense	none	0.26	0.28	0.00	No	No	not_immunogenic
NR2F2	NR2F2:p.Gly65Val	missense	none	0.24	0.12		No	No	not_immunogenic
LCE1B	LCE1B:p.Pro14Ser	missense	none	0.22	0.05		No	No	not_immunogenic
SLC8A2	SLC8A2:p.Ala33Thr	missense	none	0.22	0.05		No	No	not_immunogenic
STX8	STX8:p.Pro234Ser	missense	none	0.06	0.02		No	No	not_immunogenic
KRTAP5-4	KRTAP5-4:p.Gly34Ser	missense	none	0.00	0.05		No	No	not_immunogenic
DMKN	DMKN:p.Gly284Ser	missense	none	0.01	0.05		No	No	not_immunogenic
HLA-B	HLA-B:p.Glu100Val	missense	none			0.11	Yes	No	not_immunogenic
HLA-DRB1	HLA-DRB1:p.Tyr89Ser	missense	none			0.00	No	No	not_immunogenic