GAGE2A

G antigen 2A, the group of GAGE family

Basic information

Region (hg38): X:49589496-49596824

Previous symbols: [ "GAGE2" ]

Links

ENSG00000189064 ∙ NCBI:729447 ∙ OMIM:300720 ∙ HGNC:4099 ∙ Uniprot:Q6NT46 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GAGE2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAGE2A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			11	2		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	0

Variants in GAGE2A

This is a list of pathogenic ClinVar variants found in the GAGE2A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-49590679-G-A		not specified	Uncertain significance (May 17, 2023)
X-49590693-C-T		not specified	Uncertain significance (Feb 28, 2024)
X-49590694-G-A		not specified	Uncertain significance (Oct 21, 2021)
X-49590699-G-A		not specified	Uncertain significance (Aug 11, 2022)
X-49590700-T-C		not specified	Uncertain significance (Aug 26, 2024)
X-49590706-C-T		not specified	Uncertain significance (Feb 24, 2025)
X-49590723-C-T		not specified	Uncertain significance (Dec 03, 2024)
X-49590726-A-G		not specified	Likely benign (Feb 01, 2023)
X-49590727-T-C		not specified	Uncertain significance (Jan 30, 2024)
X-49590729-C-T		not specified	Uncertain significance (Apr 23, 2024)
X-49591225-C-T		not specified	Uncertain significance (Nov 10, 2024)
X-49591239-G-C		not specified	Uncertain significance (Jan 23, 2023)
X-49591260-C-A		not specified	Likely benign (May 13, 2024)
X-49591276-C-A		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAGE2A	protein_coding	protein_coding	ENST00000362097	4	7299

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.101	0.600	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.786	18	10.8	1.67	7.57e-7	703
Missense in Polyphen		7	3.6292	1.9288		259
Synonymous	0.581	2	3.35	0.597	2.12e-7	199
Loss of Function	0.165	1	1.19	0.837	7.57e-8	72

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 9.66e-7