Head and Neck Squamous Cell Carcinoma — Genomics

Head and Neck Squamous Cell Carcinoma — Genomics · CancerIndex

Genomics

Gene alteration frequencies by cohort

9 cohorts mapped to this entity or its descendants. Each frequency is affected / profiled within one cohort; cohorts are shown separately because case selection, sequencing depth and definitions differ. By default the cohort with the most cases profiled is shown.

Head and Neck Squamous Cell Carcinoma TCGA-HNSCTCGA

528 cases with simple somatic mutation data · 528 cases total · Data Release 46.0 · mapped to Head and Neck Squamous Cell Carcinoma ONTOLOGY_EXACT

gdcObserved30 genes · frequency = affected / profiled, as published by the cohort.

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source

Cohorts mapped to a descendant (e.g. a subtype) are included because their cases belong to this entity by definition; the mapping and its match type are shown per cohort.

Head and Neck Squamous Cell Carcinoma (Broad, Science 2011) hnsc_broadBroad

74 cases with simple somatic mutation data · 74 cases total · 2026-01-07 · mapped to Head and Neck Squamous Cell Carcinoma EXACT_IDENTIFIER

cbioportalObserved30 genes · frequency = affected / profiled, as published by the cohort.

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	TP53	Ssm	46	74	62.2%	cbioportal
2	TTN	Ssm	22	74	29.7%	cbioportal
3	SYNE1	Ssm	15	74	20.3%	cbioportal
4	MUC16	Ssm	14	74	18.9%	cbioportal
5	CSMD3	Ssm	12	74	16.2%	cbioportal
6	USH2A	Ssm	11	74	14.9%	cbioportal
7	RYR2	Ssm	10	74	13.5%	cbioportal
10	CUBN	Ssm	9	74	12.2%	cbioportal
16	ZFHX4	Ssm	9	74	12.2%	cbioportal
15	PRDM9	Ssm	9	74	12.2%	cbioportal
14	NOTCH1	Ssm	9	74	12.2%	cbioportal
13	LRP1B	Ssm	9	74	12.2%	cbioportal
12	FAT3	Ssm	9	74	12.2%	cbioportal
11	FAT1	Ssm	9	74	12.2%	cbioportal
9	COL22A1	Ssm	9	74	12.2%	cbioportal
8	CDKN2A	Ssm	9	74	12.2%	cbioportal
19	HMCN1	Ssm	8	74	10.8%	cbioportal
18	FAT4	Ssm	8	74	10.8%	cbioportal
17	FAT2	Ssm	8	74	10.8%	cbioportal
22	PCLO	Ssm	8	74	10.8%	cbioportal
21	NAV3	Ssm	8	74	10.8%	cbioportal
20	KMT2D	Ssm	8	74	10.8%	cbioportal
29	ZNF804B	Ssm	7	74	9.5%	cbioportal
27	SI	Ssm	7	74	9.5%	cbioportal
26	RIMS2	Ssm	7	74	9.5%	cbioportal
25	NSD1	Ssm	7	74	9.5%	cbioportal
24	FREM2	Ssm	7	74	9.5%	cbioportal
23	FLG	Ssm	7	74	9.5%	cbioportal
28	THSD7A	Ssm	7	74	9.5%	cbioportal
30	ADCY8	Ssm	6	74	8.1%	cbioportal

Data updated 22 days agoSource updated 2026-01-07

Head and Neck Squamous Cell Carcinoma (Johns Hopkins, Science 2011) hnsc_jhuJohns Hopkins

32 cases with simple somatic mutation data · 32 cases total · 2026-01-07 · mapped to Head and Neck Squamous Cell Carcinoma EXACT_IDENTIFIER

cbioportalObserved30 genes · frequency = affected / profiled, as published by the cohort.

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	TP53	Ssm	22	32	68.8%	cbioportal
2	NOTCH1	Ssm	4	32	12.5%	cbioportal
3	RELN	Ssm	4	32	12.5%	cbioportal
4	SYNE1	Ssm	4	32	12.5%	cbioportal
5	EPHA7	Ssm	3	32	9.4%	cbioportal
6	FLG	Ssm	3	32	9.4%	cbioportal
7	HRAS	Ssm	3	32	9.4%	cbioportal
8	PIK3AP1	Ssm	3	32	9.4%	cbioportal
9	PIK3CA	Ssm	3	32	9.4%	cbioportal
10	RIMBP2	Ssm	3	32	9.4%	cbioportal
11	SI	Ssm	3	32	9.4%	cbioportal
26	LAMA1	Ssm	2	32	6.3%	cbioportal
27	LRP1B	Ssm	2	32	6.3%	cbioportal
28	MAMDC4	Ssm	2	32	6.3%	cbioportal
29	MICAL2	Ssm	2	32	6.3%	cbioportal
30	MMP16	Ssm	2	32	6.3%	cbioportal
19	DNAI3	Ssm	2	32	6.3%	cbioportal
13	ABCD4	Ssm	2	32	6.3%	cbioportal
14	CACNA1D	Ssm	2	32	6.3%	cbioportal
15	CDKN2A	Ssm	2	32	6.3%	cbioportal
16	CELSR3	Ssm	2	32	6.3%	cbioportal
17	CR2	Ssm	2	32	6.3%	cbioportal
18	CSMD3	Ssm	2	32	6.3%	cbioportal
12	ABCA6	Ssm	2	32	6.3%	cbioportal
20	ENPP1	Ssm	2	32	6.3%	cbioportal
21	FAT4	Ssm	2	32	6.3%	cbioportal
22	FBXW7	Ssm	2	32	6.3%	cbioportal
23	GALNT14	Ssm	2	32	6.3%	cbioportal
24	GRID1	Ssm	2	32	6.3%	cbioportal
25	INSC	Ssm	2	32	6.3%	cbioportal

Data updated 22 days agoSource updated 2026-01-07

Head and Neck Squamous Cell Carcinoma (TCGA, Firehose Legacy) hnsc_tcgaTCGA

512 cases with simple somatic mutation data · 530 cases total · 2026-01-07 · mapped to Head and Neck Squamous Cell Carcinoma EXACT_IDENTIFIER

cbioportalObserved30 genes · frequency = affected / profiled, as published by the cohort.

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	TP53	Ssm	366	512	71.5%	cbioportal
2	TTN	Ssm	217	512	42.4%	cbioportal
3	FAT1	Ssm	115	512	22.5%	cbioportal
4	CDKN2A	Ssm	113	512	22.1%	cbioportal
5	FRG1BP	Ssm	106	512	20.7%	cbioportal
6	CSMD3	Ssm	105	512	20.5%	cbioportal
7	MUC16	Ssm	102	512	19.9%	cbioportal
8	PIK3CA	Ssm	94	512	18.4%	cbioportal
9	SYNE1	Ssm	92	512	18%	cbioportal
10	NOTCH1	Ssm	91	512	17.8%	cbioportal
11	LRP1B	Ssm	90	512	17.6%	cbioportal
12	KMT2D	Ssm	84	512	16.4%	cbioportal
13	PCLO	Ssm	82	512	16%	cbioportal
14	FLG	Ssm	76	512	14.8%	cbioportal
15	DNAH5	Ssm	70	512	13.7%	cbioportal
16	USH2A	Ssm	65	512	12.7%	cbioportal
17	NSD1	Ssm	62	512	12.1%	cbioportal
18	RYR2	Ssm	60	512	11.7%	cbioportal
19	PKHD1L1	Ssm	57	512	11.1%	cbioportal
20	XIRP2	Ssm	55	512	10.7%	cbioportal
22	SI	Ssm	54	512	10.5%	cbioportal
21	CASP8	Ssm	54	512	10.5%	cbioportal
23	AHNAK	Ssm	51	512	10%	cbioportal
25	FAM135B	Ssm	50	512	9.8%	cbioportal
24	DMD	Ssm	50	512	9.8%	cbioportal
26	COL11A1	Ssm	49	512	9.6%	cbioportal
27	HUWE1	Ssm	46	512	9%	cbioportal
28	PAPPA2	Ssm	46	512	9%	cbioportal
29	PCDH15	Ssm	46	512	9%	cbioportal
30	RELN	Ssm	46	512	9%	cbioportal

Data updated 22 days agoSource updated 2026-01-07

Head and Neck Squamous Cell Carcinoma (TCGA GDC, 2025) hnsc_tcga_gdcTCGA GDC

510 cases with simple somatic mutation data · 530 cases total · 2026-01-13 · mapped to Head and Neck Squamous Cell Carcinoma EXACT_IDENTIFIER

cbioportalObserved30 genes · frequency = affected / profiled, as published by the cohort.

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	TP53	Ssm	357	510	70%	cbioportal
2	TTN	Ssm	188	510	36.9%	cbioportal
3	FAT1	Ssm	108	510	21.2%	cbioportal
4	CDKN2A	Ssm	103	510	20.2%	cbioportal
5	CSMD3	Ssm	91	510	17.8%	cbioportal
6	MUC16	Ssm	90	510	17.6%	cbioportal
7	NOTCH1	Ssm	89	510	17.5%	cbioportal
8	PIK3CA	Ssm	85	510	16.7%	cbioportal
9	SYNE1	Ssm	83	510	16.3%	cbioportal
10	LRP1B	Ssm	79	510	15.5%	cbioportal
11	KMT2D	Ssm	70	510	13.7%	cbioportal
12	PCLO	Ssm	70	510	13.7%	cbioportal
13	DNAH5	Ssm	65	510	12.7%	cbioportal
14	FLG	Ssm	58	510	11.4%	cbioportal
15	USH2A	Ssm	58	510	11.4%	cbioportal
16	NSD1	Ssm	56	510	11%	cbioportal
17	CASP8	Ssm	53	510	10.4%	cbioportal
18	RYR2	Ssm	50	510	9.8%	cbioportal
19	XIRP2	Ssm	48	510	9.4%	cbioportal
20	FAM135B	Ssm	47	510	9.2%	cbioportal
21	PKHD1L1	Ssm	47	510	9.2%	cbioportal
22	AHNAK	Ssm	46	510	9%	cbioportal
24	DST	Ssm	45	510	8.8%	cbioportal
25	HUWE1	Ssm	45	510	8.8%	cbioportal
23	DMD	Ssm	45	510	8.8%	cbioportal
26	SI	Ssm	44	510	8.6%	cbioportal
27	PAPPA2	Ssm	43	510	8.4%	cbioportal
28	RELN	Ssm	43	510	8.4%	cbioportal
29	FAT3	Ssm	42	510	8.2%	cbioportal
30	COL11A1	Ssm	41	510	8%	cbioportal

Data updated 22 days agoSource updated 2026-01-13

Head and Neck Squamous Cell Carcinoma (TCGA, Nature 2015) hnsc_tcga_pubTCGA

279 cases with simple somatic mutation data · 279 cases total · 2026-01-07 · mapped to Head and Neck Squamous Cell Carcinoma EXACT_IDENTIFIER

cbioportalObserved30 genes · frequency = affected / profiled, as published by the cohort.

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	TP53	Ssm	207	279	74.2%	cbioportal
2	TTN	Ssm	127	279	45.5%	cbioportal
3	CSMD3	Ssm	66	279	23.7%	cbioportal
4	FAT1	Ssm	64	279	22.9%	cbioportal
5	CDKN2A	Ssm	63	279	22.6%	cbioportal
6	MUC16	Ssm	60	279	21.5%	cbioportal
7	PIK3CA	Ssm	58	279	20.8%	cbioportal
8	LRP1B	Ssm	57	279	20.4%	cbioportal
9	NOTCH1	Ssm	52	279	18.6%	cbioportal
10	KMT2D	Ssm	49	279	17.6%	cbioportal
11	SYNE1	Ssm	49	279	17.6%	cbioportal
12	FLG	Ssm	44	279	15.8%	cbioportal
13	DNAH5	Ssm	42	279	15.1%	cbioportal
14	PCLO	Ssm	42	279	15.1%	cbioportal
15	USH2A	Ssm	36	279	12.9%	cbioportal
16	PKHD1L1	Ssm	35	279	12.5%	cbioportal
17	SI	Ssm	32	279	11.5%	cbioportal
18	DMD	Ssm	31	279	11.1%	cbioportal
19	FRG1BP	Ssm	31	279	11.1%	cbioportal
20	RYR2	Ssm	31	279	11.1%	cbioportal
21	FAM135B	Ssm	30	279	10.8%	cbioportal
22	NSD1	Ssm	29	279	10.4%	cbioportal
23	RELN	Ssm	28	279	10%	cbioportal
24	COL11A1	Ssm	27	279	9.7%	cbioportal
25	LAMA2	Ssm	27	279	9.7%	cbioportal
26	CUBN	Ssm	26	279	9.3%	cbioportal
27	DNAH7	Ssm	26	279	9.3%	cbioportal
30	MUC17	Ssm	25	279	9%	cbioportal
28	ADGRV1	Ssm	25	279	9%	cbioportal
29	CSMD1	Ssm	25	279	9%	cbioportal

Data updated 22 days agoSource updated 2026-01-07

Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas) hnsc_tcga_pan_can_atlas_2018TCGA

515 cases with simple somatic mutation data · 523 cases total · 2026-06-23 · mapped to Head and Neck Squamous Cell Carcinoma EXACT_IDENTIFIER

cbioportalObserved30 genes · frequency = affected / profiled, as published by the cohort.

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	TP53	Ssm	357	515	69.3%	cbioportal
2	TTN	Ssm	211	515	41%	cbioportal
3	FAT1	Ssm	111	515	21.6%	cbioportal
4	CDKN2A	Ssm	105	515	20.4%	cbioportal
5	MUC16	Ssm	101	515	19.6%	cbioportal
6	CSMD3	Ssm	97	515	18.8%	cbioportal
7	PIK3CA	Ssm	90	515	17.5%	cbioportal
8	NOTCH1	Ssm	88	515	17.1%	cbioportal
9	LRP1B

Data updated 22 days agoSource updated 2026-06-23

Hereditary SDHB-Mutant Pheochromocytomas and Paragangliomas (A5 Consortium, Nature Comm 2025) hnsc_a5consortium_2025A5 Consortium

94 cases with simple somatic mutation data · 94 cases total · 2026-01-07 · mapped to Head and Neck Squamous Cell Carcinoma EXACT_IDENTIFIER

cbioportalObserved30 genes · frequency = affected / profiled, as published by the cohort.

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	SDHB	Ssm	66	94	70.2%	cbioportal
2	TERT	Ssm	18	94	19.1%	cbioportal
3	MUC17	Ssm	13	94	13.8%	cbioportal
5	TEX13C	Ssm	11	94	11.7%	cbioportal
4	GTF2I	Ssm	11	94	11.7%	cbioportal
6	ATRX	Ssm	9	94	9.6%	cbioportal
8	TCHH	Ssm	6	94	6.4%	cbioportal
7	MDC1	Ssm	6	94	6.4%	cbioportal
11	FLG2	Ssm	5	94	5.3%	cbioportal
12	OBSCN	Ssm	5	94	5.3%	cbioportal
10	FAM47C	Ssm	5	94	5.3%	cbioportal
9	BLOC1S5-TXNDC5	Ssm	5	94	5.3%	cbioportal
21	MUC5AC	Ssm	4	94	4.3%	cbioportal
13	ADAMTS2	Ssm	4	94	4.3%	cbioportal
14	BCOR	Ssm	4	94	4.3%	cbioportal
15	BCR	Ssm	4	94	4.3%	cbioportal
16	CACNA1A	Ssm	4	94	4.3%	cbioportal
17	CACNA1E	Ssm	4	94	4.3%	cbioportal
18	DST	Ssm	4	94	4.3%	cbioportal
19	LINC01618	Ssm	4	94	4.3%	cbioportal
20	MED12	Ssm	4	94	4.3%	cbioportal
22	NBPF11	Ssm	4	94	4.3%	cbioportal
23	NOX5	Ssm	4	94	4.3%	cbioportal
24	PCNT	Ssm	4	94	4.3%	cbioportal
25	PRR5-ARHGAP8	Ssm	4	94	4.3%	cbioportal
26	SECISBP2L	Ssm	4	94	4.3%	cbioportal
27	TTN	Ssm	4	94	4.3%	cbioportal
30	ANKRD30B	Ssm	3	94	3.2%	cbioportal
29	AMOTL2	Ssm	3	94	3.2%	cbioportal
28	AHNAK	Ssm	3	94	3.2%	cbioportal

Data updated 22 days agoSource updated 2026-01-07

Oral Squamous Cell Carcinoma (MD Anderson, Cancer Discov 2013) hnsc_mdanderson_2013MD Anderson

40 cases with simple somatic mutation data · 40 cases total · 2026-01-07 · mapped to Head and Neck Squamous Cell Carcinoma EXACT_IDENTIFIER

cbioportalObserved30 genes · frequency = affected / profiled, as published by the cohort.

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	TP53	Ssm	19	40	47.5%	cbioportal
2	TTN	Ssm	5	40	12.5%	cbioportal
3	FAT1	Ssm	4	40	10%	cbioportal
4	OR2T35	Ssm	4	40	10%	cbioportal
7	GPRIN2	Ssm	3	40	7.5%	cbioportal
5	ARHGAP29	Ssm	3	40	7.5%	cbioportal
8	RYR2	Ssm	3	40	7.5%	cbioportal
6	EPHA7	Ssm	3	40	7.5%	cbioportal
9	ABCA6	Ssm	2	40	5%	cbioportal
29	HCRTR2	Ssm	2	40	5%	cbioportal
28	GDF2	Ssm	2	40	5%	cbioportal
30	HLA-B	Ssm	2	40	5%	cbioportal
18	COL11A1	Ssm	2	40	5%	cbioportal
19	CRABP2	Ssm	2	40	5%	cbioportal
20	CSMD3	Ssm	2	40	5%	cbioportal
21	DCC	Ssm	2	40	5%	cbioportal
22	DMKN	Ssm	2	40	5%	cbioportal
23	DSC1	Ssm	2	40	5%	cbioportal
25	EPG5	Ssm	2	40	5%	cbioportal
24	EGFR	Ssm	2	40	5%	cbioportal
26	ERICH3	Ssm	2	40	5%	cbioportal
27	GALNT14	Ssm	2	40	5%	cbioportal
17	CASP8	Ssm	2	40	5%	cbioportal
16	CACNA1D	Ssm	2	40	5%	cbioportal
15	BBS9	Ssm	2	40	5%	cbioportal
14	ALPI	Ssm	2	40	5%	cbioportal
13	AKAP12	Ssm	2	40	5%	cbioportal
12	AHNAK2	Ssm	2	40	5%	cbioportal
11	ACSF3	Ssm	2	40	5%	cbioportal
10	ABR	Ssm	2	40	5%	cbioportal

Data updated 22 days agoSource updated 2026-01-07