Malignant Esophageal Neoplasm — Genomics

Malignant Esophageal Neoplasm — Genomics · CancerIndex

Genomics

Gene alteration frequencies by cohort

7 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.

Esophageal Adenocarcinoma (DFCI, Nat Genet 2013) esca_broadDFCI

151 cases with simple somatic mutation data · 151 cases total · 2026-01-07 · mapped to Esophageal Adenocarcinoma EXACT_IDENTIFIER

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

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	TP53

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.

Esophageal Adenocarcinoma (TCGA GDC, 2025) esca_tcga_gdcTCGA GDC

185 cases with simple somatic mutation data · 186 cases total · 2026-01-13 · mapped to Esophageal Adenocarcinoma EXACT_IDENTIFIER

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

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	TP53	Ssm	156	185	84.3%	cbioportal
2	TTN	Ssm	75	185	40.5%	cbioportal
3	MUC16	Ssm	40	185	21.6%	cbioportal
4	CSMD3	Ssm	35	185	18.9%	cbioportal
5	SYNE1	Ssm	33	185	17.8%	cbioportal
7	LRP1B	Ssm	27	185	14.6%	cbioportal
6	FLG	Ssm	27	185	14.6%	cbioportal
8	DNAH5	Ssm	26	185	14.1%	cbioportal
9	PCLO	Ssm	25	185	13.5%	cbioportal
10	HMCN1	Ssm	24	185	13%	cbioportal
12	RYR2	Ssm	22	185	11.9%	cbioportal
11	KMT2D	Ssm	22	185	11.9%	cbioportal
13	CSMD1	Ssm	20	185	10.8%	cbioportal
15	ZNF804B	Ssm	19	185	10.3%	cbioportal
14	FAT3	Ssm	19	185	10.3%	cbioportal
18	UNC13C	Ssm	18	185	9.7%	cbioportal
17	SPTA1	Ssm	18	185	9.7%	cbioportal
16	SACS	Ssm	18	185	9.7%	cbioportal
21	RYR3	Ssm	17	185	9.2%	cbioportal
20	NOTCH1	Ssm	17	185	9.2%	cbioportal
19	NFE2L2	Ssm	17	185	9.2%	cbioportal
26	PCDH15	Ssm	16	185	8.6%	cbioportal
24	LAMA1	Ssm	16	185	8.6%	cbioportal
22	COL11A1	Ssm	16	185	8.6%	cbioportal
23	DYNC2H1	Ssm	16	185	8.6%	cbioportal
27	PIK3CA	Ssm	16	185	8.6%	cbioportal
25	OBSCN	Ssm	16	185	8.6%	cbioportal
29	ARID1A	Ssm	15	185	8.1%	cbioportal
28	ADGRV1	Ssm	15	185	8.1%	cbioportal
30	CNTNAP5	Ssm	15	185	8.1%	cbioportal

Data updated 22 days agoSource updated 2026-01-13

Esophageal Adenocarcinoma (TCGA, PanCancer Atlas) esca_tcga_pan_can_atlas_2018TCGA

182 cases with simple somatic mutation data · 182 cases total · 2026-06-05 · mapped to Esophageal Adenocarcinoma EXACT_IDENTIFIER

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

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	TP53	Ssm	158	182	86.8%	cbioportal
2	TTN	Ssm	75	182	41.2%	cbioportal
3	MUC16	Ssm	43	182	23.6%	cbioportal
4	SYNE1	Ssm	37	182	20.3%	cbioportal
5	CSMD3	Ssm	35	182	19.2%	cbioportal
6	FLG	Ssm	32	182	17.6%	cbioportal
7	HMCN1	Ssm	31	182	17%	cbioportal
8	LRP1B	Ssm	31	182	17%	cbioportal
9	DNAH5	Ssm	30	182	16.5%	cbioportal
10	PCLO	Ssm	27	182	14.8%	cbioportal
11	RYR2	Ssm	23	182	12.6%	cbioportal
13	KMT2D	Ssm	22	182	12.1%	cbioportal
12	EYS	Ssm	22	182	12.1%	cbioportal
14	CSMD1	Ssm	21	182	11.5%	cbioportal
17	SPTA1	Ssm	20	182	11%	cbioportal
18	UNC13C	Ssm	20	182	11%	cbioportal
15	FAT3	Ssm	20	182	11%	cbioportal
16	PKHD1L1	Ssm	20	182	11%	cbioportal
20	OBSCN	Ssm	19	182	10.4%	cbioportal
19	DYNC2H1	Ssm	19	182	10.4%	cbioportal
21	PCDH15	Ssm	19	182	10.4%	cbioportal
22	ZNF804B	Ssm	19	182	10.4%	cbioportal
23	NFE2L2	Ssm	18	182	9.9%	cbioportal
24	SACS	Ssm	18	182	9.9%	cbioportal
25	USH2A	Ssm	18	182	9.9%	cbioportal
26	CNTNAP5	Ssm	17	182	9.3%	cbioportal
27	LAMA1	Ssm	17	182	9.3%	cbioportal
28	LRRK2	Ssm	17	182	9.3%	cbioportal
29	MUC4	Ssm	17	182	9.3%	cbioportal
30	PIK3CA	Ssm	17	182	9.3%	cbioportal

Data updated 22 days agoSource updated 2026-06-05

Esophageal Carcinoma TCGA-ESCATCGA

185 cases with simple somatic mutation data · 185 cases total · Data Release 46.0 · mapped to Esophageal Carcinoma ONTOLOGY_EXACT

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

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	TP53	Ssm	167	185	90.3%	gdc
2	MYC	Ssm	138	185	74.6%	gdc
3	POU5F1B	Ssm	138	185	74.6%	gdc
4	TG	Ssm	138	185	74.6%	gdc
5	KCNQ3	Ssm	135	185	73%	gdc
6	GSDMC	Ssm	134	185	72.4%	gdc
7	ADCY8	Ssm	134	185	72.4%	gdc
8	CDKN2A	Ssm	134	185	72.4%	gdc
9	LRATD2	Ssm	134	185	72.4%	gdc
10	EFR3A	Ssm	133	185	71.9%	gdc
11	CDKN2B	Ssm	133	185	71.9%	gdc
14	TRIB1	Ssm	132	185	71.4%	gdc
22	OC90	Ssm	132	185	71.4%	gdc
12	NDRG1	Ssm	132	185	71.4%	gdc
15	ASAP1	Ssm	132	185	71.4%	gdc
16	HHLA1	Ssm	132	185	71.4%	gdc
17	CCN4	Ssm	132	185	71.4%	gdc
18	ZFAT	Ssm	132	185	71.4%	gdc
19	LRRC6	Ssm	132	185	71.4%	gdc
20	AC100868.1	Ssm	132	185	71.4%	gdc
21	SLA	Ssm	132	185	71.4%	gdc
13	KHDRBS3	Ssm	132	185	71.4%	gdc
23	COL22A1	Ssm	131	185	70.8%	gdc
25	ZNF572	Ssm	131	185	70.8%	gdc
26	WASHC5	Ssm	131	185	70.8%	gdc
27	TMEM71	Ssm	131	185	70.8%	gdc
24	PHF20L1	Ssm	131	185	70.8%	gdc
28	CYRIB	Ssm	131	185	70.8%	gdc
29	ST3GAL1	Ssm	131	185	70.8%	gdc
41	PDCD10	Ssm	130	185	70.3%	gdc

Data updated 22 days agoSource updated Data Release 46.0

Esophageal Carcinoma (TCGA, Firehose Legacy) esca_tcgaTCGA

185 cases with simple somatic mutation data · 186 cases total · 2026-01-07 · mapped to Esophageal Adenocarcinoma EXACT_IDENTIFIER

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

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	TP53	Ssm	153	185	82.7%	cbioportal
2	TTN	Ssm	97	185	52.4%	cbioportal
3	MUC16	Ssm	51	185	27.6%	cbioportal
4	SYNE1	Ssm	44	185	23.8%	cbioportal
5	CSMD3	Ssm	40	185	21.6%	cbioportal
6	DNAH5	Ssm	35	185	18.9%	cbioportal
7	HMCN1	Ssm	34	185	18.4%	cbioportal
8	LRP1B	Ssm	33	185	17.8%	cbioportal
10	KMT2D	Ssm	32	185	17.3%	cbioportal
9	FLG	Ssm	32	185	17.3%	cbioportal
11	RYR2	Ssm	31	185	16.8%	cbioportal
13	PCLO	Ssm	29	185	15.7%	cbioportal
12	MUC4	Ssm	29	185	15.7%	cbioportal
14	USH2A	Ssm	29	185	15.7%	cbioportal
16	OBSCN	Ssm	27	185	14.6%	cbioportal
15	CSMD1	Ssm	27	185	14.6%	cbioportal
17	PKHD1L1	Ssm	26	185	14.1%	cbioportal
20	SPTA1	Ssm	25	185	13.5%	cbioportal
18	FAT3	Ssm	25	185	13.5%	cbioportal
19	FAT4	Ssm	25	185	13.5%	cbioportal
21	MUC12	Ssm	24	185	13%	cbioportal
23	RYR3	Ssm	23	185	12.4%	cbioportal
22	DYNC2H1	Ssm	23	185	12.4%	cbioportal
24	XIRP2	Ssm	23	185	12.4%	cbioportal
25	ADGRV1	Ssm	22	185	11.9%	cbioportal
26	DST	Ssm	22	185	11.9%	cbioportal
29	EYS	Ssm	21	185	11.4%	cbioportal
27	ATM	Ssm	21	185	11.4%	cbioportal
28	CDKN2A	Ssm	21	185	11.4%	cbioportal
30	NEB	Ssm	21	185	11.4%	cbioportal

Data updated 22 days agoSource updated 2026-01-07

Esophageal Squamous Cell Carcinoma (ICGC, Nature 2014) escc_icgcICGC

88 cases with simple somatic mutation data · 88 cases total · 2026-01-07 · mapped to Esophageal 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	73	88	83%	cbioportal
2	TTN	Ssm	28	88	31.8%	cbioportal
3	MUC16	Ssm	12	88	13.6%	cbioportal
4	PCLO	Ssm	12	88	13.6%	cbioportal
5	ZFHX4	Ssm	11	88	12.5%	cbioportal
6	LRP1B	Ssm	10	88	11.4%	cbioportal
7	DMD	Ssm	8	88	9.1%	cbioportal
8	NOTCH1	Ssm	8	88	9.1%	cbioportal
9	CSMD3	Ssm	7	88	8%	cbioportal
10	DNAH6	Ssm	7	88	8%	cbioportal
11	PKHD1L1	Ssm	7	88	8%	cbioportal
12	RB1	Ssm	7	88	8%	cbioportal
13	SYNE1	Ssm	7	88	8%	cbioportal
14	ADGRV1	Ssm	6	88	6.8%	cbioportal
15	CACNA1E	Ssm	6	88	6.8%	cbioportal
16	DNAH14	Ssm	6	88	6.8%	cbioportal
17	DNAH17	Ssm	6	88	6.8%	cbioportal
18	FAM135B	Ssm	6	88	6.8%	cbioportal
19	FAT3	Ssm	6	88	6.8%	cbioportal
20	FAT4	Ssm	6	88	6.8%	cbioportal
21	MACF1	Ssm	6	88	6.8%	cbioportal
22	RP1	Ssm	6	88	6.8%	cbioportal
23	RYR2	Ssm	6	88	6.8%	cbioportal
24	USH2A	Ssm	6	88	6.8%	cbioportal
25	ABCA13	Ssm	5	88	5.7%	cbioportal
26	ADGB	Ssm	5	88	5.7%	cbioportal
27	CACNA1A	Ssm	5	88	5.7%	cbioportal
28	COL24A1	Ssm	5	88	5.7%	cbioportal
29	COL6A3	Ssm	5	88	5.7%	cbioportal
30	CREBBP	Ssm	5	88	5.7%	cbioportal

Data updated 22 days agoSource updated 2026-01-07

Esophageal Squamous Cell Carcinoma (UCLA, Nat Genet 2014) escc_ucla_2014UCLA

139 cases with simple somatic mutation data · 139 cases total · 2026-01-07 · mapped to Esophageal 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	83	139	59.7%	cbioportal
2	TTN	Ssm	49	139	35.3%	cbioportal
152	MYH2	Ssm	4	20	20%	cbioportal
180	ZNF676	Ssm	4	20	20%	cbioportal
3	KMT2D	Ssm	25	139	18%	cbioportal
4	MUC16	Ssm	20	139	14.4%	cbioportal
5	SYNE1	Ssm	18	139	12.9%	cbioportal
6	FAT1	Ssm	16	139	11.5%	cbioportal
8	CSMD3	Ssm	15	139	10.8%	cbioportal
9	LRP1B	Ssm	15	139	10.8%	cbioportal
7	ADGRV1	Ssm	15	139	10.8%	cbioportal
10	PCLO	Ssm	14	139	10.1%	cbioportal
11	XIRP2	Ssm	13	139	9.4%	cbioportal
12	ABCA13	Ssm	12	139	8.6%	cbioportal
13	FAT2	Ssm	12	139	8.6%	cbioportal
14	HMCN1	Ssm	12	139	8.6%	cbioportal
15	MUC4	Ssm	12	139	8.6%	cbioportal
24	NOTCH1	Ssm	11	139	7.9%	cbioportal
25	PIK3CA	Ssm	11	139	7.9%	cbioportal
26	RB1	Ssm	11	139	7.9%	cbioportal
18	EP300	Ssm	11	139	7.9%	cbioportal
19	FSIP2	Ssm	11	139	7.9%	cbioportal
20	KMT2C	Ssm	11	139	7.9%	cbioportal
21	LRP2	Ssm	11	139	7.9%	cbioportal
22	MUC17	Ssm	11	139	7.9%	cbioportal
23	MUC2	Ssm	11	139	7.9%	cbioportal
16	DMD	Ssm	11	139	7.9%	cbioportal
17	DNAH5	Ssm	11	139	7.9%	cbioportal
30	SYNE2	Ssm	10	139	7.2%	cbioportal
29	HYDIN	Ssm	10	139	7.2%	cbioportal

Data updated 22 days agoSource updated 2026-01-07