Malignant Central Nervous System Neoplasm — Genomics

Malignant Central Nervous System Neoplasm — Genomics · CancerIndex

Genomics

Gene alteration frequencies by cohort

10 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.

Glioblastoma Multiforme TCGA-GBMTCGA

601 cases with simple somatic mutation data · 617 cases total · Data Release 46.0 · mapped to Glioblastoma CURATED_BROADER

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

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

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.

Medulloblastoma (Broad, Nature 2012) mbl_broad_2012Broad

92 cases with simple somatic mutation data · 92 cases total · 2026-01-07 · mapped to Medulloblastoma EXACT_IDENTIFIER

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

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	KMT2D	Ssm	8	92	8.7%	cbioportal
2	DDX3X	Ssm	7	92	7.6%	cbioportal
3	CTNNB1	Ssm	6	92	6.5%	cbioportal
4	PTCH1	Ssm	6	92	6.5%	cbioportal
5	ABCA13	Ssm	4	92	4.3%	cbioportal
6	KMT2C	Ssm	4	92	4.3%	cbioportal
7	SMARCA4	Ssm	4	92	4.3%	cbioportal
8	BCOR	Ssm	3	92	3.3%	cbioportal
9	EPPK1	Ssm	3	92	3.3%	cbioportal
10	GPS2	Ssm	3	92	3.3%	cbioportal
11	KDM6A	Ssm	3	92	3.3%	cbioportal
12	LAMA5	Ssm	3	92	3.3%	cbioportal
13	MAN2C1	Ssm	3	92	3.3%	cbioportal
14	PLXNA2	Ssm	3	92	3.3%	cbioportal
15	SPTB	Ssm	3	92	3.3%	cbioportal
16	TP53	Ssm	3	92	3.3%	cbioportal
17	TTN	Ssm	3	92	3.3%	cbioportal
29	CSF2RA	Ssm	2	92	2.2%	cbioportal
18	ABCA2	Ssm	2	92	2.2%	cbioportal
19	ABCA8	Ssm	2	92	2.2%	cbioportal
20	ABCC6	Ssm	2	92	2.2%	cbioportal
21	ADAMTS12	Ssm	2	92	2.2%	cbioportal
22	ADD2	Ssm	2	92	2.2%	cbioportal
23	ADGRE2	Ssm	2	92	2.2%	cbioportal
24	ADH7	Ssm	2	92	2.2%	cbioportal
25	AHNAK	Ssm	2	92	2.2%	cbioportal
26	ASAP3	Ssm	2	92	2.2%	cbioportal
27	BAIAP3	Ssm	2	92	2.2%	cbioportal
28	CLEC12B	Ssm	2	92	2.2%	cbioportal
30	CTDNEP1	Ssm	2	92	2.2%	cbioportal

Data updated 22 days agoSource updated 2026-01-07

Medulloblastoma (DKFZ, Nature 2017) mbl_dkfz_2017DKFZ

491 cases with simple somatic mutation data · 491 cases total · 2026-01-16 · mapped to Medulloblastoma EXACT_IDENTIFIER

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

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	PTCH1	Ssm	51	491	10.4%	cbioportal
2	TERT	Ssm	50	491	10.2%	cbioportal
3	DDX3X	Ssm	43	491	8.8%	cbioportal
4	KMT2D	Ssm	34	491	6.9%	cbioportal
5	CTNNB1	Ssm	32	491	6.5%	cbioportal
6	KMT2C	Ssm	29	491	5.9%	cbioportal
7	SMARCA4	Ssm	25	491	5.1%	cbioportal
8	TTN	Ssm	23	491	4.7%	cbioportal
9	KBTBD4	Ssm	19	491	3.9%	cbioportal
10	KDM6A	Ssm	17	491	3.5%	cbioportal
11	MUC16	Ssm	17	491	3.5%	cbioportal
12	TP53	Ssm	17	491	3.5%	cbioportal
13	CREBBP	Ssm	15	491	3.1%	cbioportal
14	ZMYM3	Ssm	14	491	2.9%	cbioportal
15	SMO	Ssm	13	491	2.6%	cbioportal
16	TCF4	Ssm	12	491	2.4%	cbioportal
17	ZIC1	Ssm	12	491	2.4%	cbioportal
18	CDK1	Ssm	11	491	2.2%	cbioportal
19	NIN	Ssm	11	491	2.2%	cbioportal
20	NME5	Ssm	11	491	2.2%	cbioportal
21	FBXW7	Ssm	10	491	2%	cbioportal
22	GSE1	Ssm	10	491	2%	cbioportal
23	LAMA2	Ssm	10	491	2%	cbioportal
24	RSBN1L	Ssm	10	491	2%	cbioportal
25	CTDNEP1	Ssm	9	491	1.8%	cbioportal
26	PIK3CA	Ssm	9	491	1.8%	cbioportal
27	BCOR	Ssm	8	491	1.6%	cbioportal
28	MUC17	Ssm	8	491	1.6%	cbioportal
29	RYR3	Ssm	8	491	1.6%	cbioportal
30	ARID1A	Ssm	7	491	1.4%	cbioportal

Data updated 22 days agoSource updated 2026-01-16

Medulloblastoma (ICGC, Nature 2012) mbl_icgcICGC

125 cases with simple somatic mutation data · 125 cases total · 2026-01-07 · mapped to Medulloblastoma EXACT_IDENTIFIER

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

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	CTNNB1	Ssm	15	125	12%	cbioportal
2	DDX3X	Ssm	10	125	8%	cbioportal
3	PTCH1	Ssm	8	125	6.4%	cbioportal
4	KMT2D	Ssm	6	125	4.8%	cbioportal
5	SMARCA4	Ssm	6	125	4.8%	cbioportal
6	KDM6A	Ssm	5	125	4%	cbioportal
7	TP53	Ssm	5	125	4%	cbioportal
8	CTDNEP1	Ssm	4	125	3.2%	cbioportal
9	CEP83	Ssm	3	125	2.4%	cbioportal
10	CUBN	Ssm	3	125	2.4%	cbioportal
11	FRAS1	Ssm	3	125	2.4%	cbioportal
12	KMT2C	Ssm	3	125	2.4%	cbioportal
13	NF1	Ssm	3	125	2.4%	cbioportal
14	TLN2	Ssm	3	125	2.4%	cbioportal
15	TRPC3	Ssm	3	125	2.4%	cbioportal
16	ABCA4	Ssm	2	125	1.6%	cbioportal
17	AKAP11	Ssm	2	125	1.6%	cbioportal
18	ALPK2	Ssm	2	125	1.6%	cbioportal
19	ANGEL2	Ssm	2	125	1.6%	cbioportal
20	AOC3	Ssm	2	125	1.6%	cbioportal
21	ARID1B	Ssm	2	125	1.6%	cbioportal
22	BCLAF1	Ssm	2	125	1.6%	cbioportal
23	BCOR	Ssm	2	125	1.6%	cbioportal
24	CBFA2T2	Ssm	2	125	1.6%	cbioportal
25	CCAR1	Ssm	2	125	1.6%	cbioportal
26	CDH10	Ssm	2	125	1.6%	cbioportal
27	CLCN2	Ssm	2	125	1.6%	cbioportal
28	CLDN24	Ssm	2	125	1.6%	cbioportal
29	CPAMD8	Ssm	2	125	1.6%	cbioportal
30	DLG5	Ssm	2	125	1.6%	cbioportal

Data updated 22 days agoSource updated 2026-01-07

Medulloblastoma (PCGP, Nature 2012) mbl_pcgpPCGP

37 cases with simple somatic mutation data · 37 cases total · 2026-01-07 · mapped to Medulloblastoma EXACT_IDENTIFIER

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

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	CTNNB1	Ssm	4	37	10.8%	cbioportal
2	DDX3X	Ssm	4	37	10.8%	cbioportal
3	CHD7	Ssm	3	37	8.1%	cbioportal
4	KDM6A	Ssm	3	37	8.1%	cbioportal
5	TTN	Ssm	3	37	8.1%	cbioportal
6	CACNA1D	Ssm	2	37	5.4%	cbioportal
7	DEPDC5	Ssm	2	37	5.4%	cbioportal
8	DNAH14	Ssm	2	37	5.4%	cbioportal
9	DYNC1H1	Ssm	2	37	5.4%	cbioportal
10	FAP	Ssm	2	37	5.4%	cbioportal
11	FCRL2	Ssm	2	37	5.4%	cbioportal
12	GPAM	Ssm	2	37	5.4%	cbioportal
13	IFIT3	Ssm	2	37	5.4%	cbioportal
14	PFKP	Ssm	2	37	5.4%	cbioportal
15	SF3B1	Ssm	2	37	5.4%	cbioportal
16	WDFY3	Ssm	2	37	5.4%	cbioportal
17	WDFY4	Ssm	2	37	5.4%	cbioportal
18	ZMYM3	Ssm	2	37	5.4%	cbioportal
91	CSMD3	Ssm	1	37	2.7%	cbioportal
19	ABCA4	Ssm	1	37	2.7%	cbioportal
20	ABCB9	Ssm	1	37	2.7%	cbioportal
21	ABCG2	Ssm	1	37	2.7%	cbioportal
22	ABI3BP	Ssm	1	37	2.7%	cbioportal
23	ACAN	Ssm	1	37	2.7%	cbioportal
24	ADAMTS20	Ssm	1	37	2.7%	cbioportal
25	ADGRB3	Ssm	1	37	2.7%	cbioportal
26	AGGF1	Ssm	1	37	2.7%	cbioportal
27	AKAP9	Ssm	1	37	2.7%	cbioportal
28	AKR1B10	Ssm	1	37	2.7%	cbioportal
29	ALDH1L1	Ssm	1	37	2.7%	cbioportal

Data updated 22 days agoSource updated 2026-01-07

Medulloblastoma (Sickkids, Nature 2016) mbl_sickkids_2016Sickkids

46 cases with simple somatic mutation data · 46 cases total · 2026-01-07 · mapped to Medulloblastoma EXACT_IDENTIFIER

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

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	TTN	Ssm	9	46	19.6%	cbioportal
2	MUC4	Ssm	7	46	15.2%	cbioportal
3	TP53	Ssm	6	46	13%	cbioportal
8	VWA5B2	Ssm	5	46	10.9%	cbioportal
5	MUC16	Ssm	5	46	10.9%	cbioportal
6	MUC6	Ssm	5	46	10.9%	cbioportal
7	TG	Ssm	5	46	10.9%	cbioportal
4	CREBBP	Ssm	5	46	10.9%	cbioportal
13	KMT2D	Ssm	4	46	8.7%	cbioportal
14	MUC2	Ssm	4	46	8.7%	cbioportal
11	FBXW7	Ssm	4	46	8.7%	cbioportal
15	PTCH1	Ssm	4	46	8.7%	cbioportal
16	RYR3	Ssm	4	46	8.7%	cbioportal
17	USH2A	Ssm	4	46	8.7%	cbioportal
18	VEPH1	Ssm	4	46	8.7%	cbioportal
10	ALAS1	Ssm	4	46	8.7%	cbioportal
9	ABCA13	Ssm	4	46	8.7%	cbioportal
12	FRAS1	Ssm	4	46	8.7%	cbioportal
36	KIAA1614	Ssm	3	46	6.5%	cbioportal
37	KNL1	Ssm	3	46	6.5%	cbioportal
38	LAMC1	Ssm	3	46	6.5%	cbioportal
39	MED12	Ssm	3	46	6.5%	cbioportal
40	MICAL2	Ssm	3	46	6.5%	cbioportal
41	MKI67	Ssm	3	46	6.5%	cbioportal
42	MSH6	Ssm	3	46	6.5%	cbioportal
43	MUC12	Ssm	3	46	6.5%	cbioportal
44	NEB	Ssm	3	46	6.5%	cbioportal
45	PHLDB2	Ssm	3	46	6.5%	cbioportal
46	PKHD1L1	Ssm	3	46	6.5%	cbioportal
47	PLCB2	Ssm	3	46	6.5%	cbioportal

Data updated 22 days agoSource updated 2026-01-07

Primary Central Nervous System Lymphoma (Mayo Clinic, Clin Cancer Res 2015) pcnsl_mayo_2015Mayo Clinic

10 cases with simple somatic mutation data · 19 cases total · 2026-01-12 · mapped to Primary Central Nervous System Lymphoma EXACT_IDENTIFIER

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

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	MYD88	Ssm	7	10	70%	cbioportal
2	CD79B	Ssm	4	10	40%	cbioportal
3	DLGAP2	Ssm	4	10	40%	cbioportal
4	PIM1	Ssm	4	10	40%	cbioportal
5	SMG5	Ssm	4	10	40%	cbioportal
6	BTG2	Ssm	3	10	30%	cbioportal
7	CARD11	Ssm	3	10	30%	cbioportal
8	DSG4	Ssm	3	10	30%	cbioportal
9	DST	Ssm	3	10	30%	cbioportal
10	FAT4	Ssm	3	10	30%	cbioportal
11	KLHL14	Ssm	3	10	30%	cbioportal
12	LRP1B	Ssm	3	10	30%	cbioportal
13	PRR12	Ssm	3	10	30%	cbioportal
14	TCL1A	Ssm	3	10	30%	cbioportal
15	TENM1	Ssm	3	10	30%	cbioportal
16	A2ML1	Ssm	2	10	20%	cbioportal
17	AHNAK	Ssm	2	10	20%	cbioportal
18	ANGPTL6	Ssm	2	10	20%	cbioportal
19	APBA1	Ssm	2	10	20%	cbioportal
20	ARAF	Ssm	2	10	20%	cbioportal
21	BCL2	Ssm	2	10	20%	cbioportal
22	BSN	Ssm	2	10	20%	cbioportal
23	BTG1	Ssm	2	10	20%	cbioportal
24	C10ORF71	Ssm	2	10	20%	cbioportal
25	CCDC7	Ssm	2	10	20%	cbioportal
26	CDKN1B	Ssm	2	10	20%	cbioportal
27	CEP295	Ssm	2	10	20%	cbioportal
28	CFAP47	Ssm	2	10	20%	cbioportal
29	CHPF2	Ssm	2	10	20%	cbioportal
30	CNTNAP5	Ssm	2	10	20%	cbioportal

Data updated 22 days agoSource updated 2026-01-12

Primary CNS Lymphoma (MSK, Clin Cancer Res 2024) pcnsl_msk_2024MSK

86 cases with simple somatic mutation data · 86 cases total · 2026-01-12 · mapped to Primary Central Nervous System Lymphoma EXACT_IDENTIFIER

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

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	MYD88	Ssm	37	86	43%	cbioportal
2	PIM1	Ssm	33	86	38.4%	cbioportal
3	CD79B	Ssm	20	86	23.3%	cbioportal
4	KMT2D	Ssm	20	86	23.3%	cbioportal
5	DTX1	Ssm	18	86	20.9%	cbioportal
6	H1-4	Ssm	16	86	18.6%	cbioportal
7	BTG2	Ssm	15	86	17.4%	cbioportal
9	ETV6	Ssm	14	86	16.3%	cbioportal
10	TBL1XR1	Ssm	14	86	16.3%	cbioportal
8	BTG1	Ssm	14	86	16.3%	cbioportal
11	HLA-A	Ssm	13	86	15.1%	cbioportal
12	SETD1B	Ssm	12	86	14%	cbioportal
13	GNA13	Ssm	11	86	12.8%	cbioportal
14	SOCS1	Ssm	10	86	11.6%	cbioportal
16	CARD11	Ssm	9	86	10.5%	cbioportal
17	IRF4	Ssm	9	86	10.5%	cbioportal
15	B2M	Ssm	9	86	10.5%	cbioportal
18	MPEG1	Ssm	9	86	10.5%	cbioportal
20	H1-2	Ssm	8	86	9.3%	cbioportal
19	CREBBP	Ssm	8	86	9.3%	cbioportal
26	PCBP1	Ssm	7	86	8.1%	cbioportal
21	CCND3	Ssm	7	86	8.1%	cbioportal
22	CXCR4	Ssm	7	86	8.1%	cbioportal
23	FAT1	Ssm	7	86	8.1%	cbioportal
24	KMT2C	Ssm	7	86	8.1%	cbioportal
25	LTB	Ssm	7	86	8.1%	cbioportal
27	PCLO	Ssm	7	86	8.1%	cbioportal
28	PHOX2B	Ssm	7	86	8.1%	cbioportal
29	TP53	Ssm	7	86	8.1%	cbioportal
31	DDX3X	Ssm	6	86	7%	cbioportal

Data updated 22 days agoSource updated 2026-01-12

Retinoblastoma cfDNA (MSK, Cancer Med 2020) rbl_cfdna_msk_2020MSK

14 cases with simple somatic mutation data · 14 cases total · 2026-01-16 · mapped to Retinoblastoma EXACT_IDENTIFIER

cbioportalObserved2 genes · frequency = affected / profiled, as published by the cohort.

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	RB1	Ssm	14	14	100%	cbioportal
2	MYCN	Ssm	9	14	64.3%	cbioportal

Data updated 22 days agoSource updated 2026-01-16

Retinoblastoma (MSK, Cancers 2021) rbl_mskcc_2020MSK

83 cases with simple somatic mutation data · 83 cases total · 2026-01-16 · mapped to Retinoblastoma EXACT_IDENTIFIER

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

#	Gene	Alteration	Affected (n)	Profiled (n)	Frequency (%)	Source
1	RB1	Ssm	52	83	62.7%	cbioportal
2	BCOR	Ssm	14	83	16.9%	cbioportal
6	RPTOR	Ssm	3	83	3.6%	cbioportal
7	ZFHX3	Ssm	3	83	3.6%	cbioportal
4	BRD4	Ssm	3	83	3.6%	cbioportal
3	ARID1A	Ssm	3	83	3.6%	cbioportal
5	FAT1	Ssm	3	83	3.6%	cbioportal
19	PREX2	Ssm	2	78	2.6%	cbioportal
13	MSH3	Ssm	2	78	2.6%	cbioportal
18	POLE	Ssm	2	83	2.4%	cbioportal
20	TERT	Ssm	2	83	2.4%	cbioportal
8	ARID1B	Ssm	2	83	2.4%	cbioportal
9	HLA-A	Ssm	2	83	2.4%	cbioportal
10	KMT2C	Ssm	2	83	2.4%	cbioportal
11	KMT2D	Ssm	2	83	2.4%	cbioportal
12	MAP3K1	Ssm	2	83	2.4%	cbioportal
14	NCOA3	Ssm	2	83	2.4%	cbioportal
15	NSD1	Ssm	2	83	2.4%	cbioportal
16	PIK3CD	Ssm	2	83	2.4%	cbioportal
17	POLD1	Ssm	2	83	2.4%	cbioportal
78	WHR1	Ssm	1	78	1.3%	cbioportal
25	BABAM1	Ssm	1	78	1.3%	cbioportal
30	CARM1	Ssm	1	78	1.3%	cbioportal
63	PRKD1	Ssm	1	78	1.3%	cbioportal
66	RAC2	Ssm	1	78	1.3%	cbioportal
67	RRAGC	Ssm	1	78	1.3%	cbioportal
68	RTEL1	Ssm	1	78	1.3%	cbioportal
74	TEK	Ssm	1	78	1.3%	cbioportal
76	TP53BP1	Ssm	1	78	1.3%	cbioportal
72	SOX17	Ssm	1	83	1.2%	cbioportal

Data updated 22 days agoSource updated 2026-01-16