GAGE10

G antigen 10, the group of GAGE family

Basic information

Region (hg38): X:49303646-49319841

Links

ENSG00000215274 ∙ NCBI:102724473 ∙ OMIM:300737 ∙ HGNC:30968 ∙ Uniprot:A6NGK3 ∙ 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 GAGE10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAGE10 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				1		1
missense			13			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	13	1	0

Variants in GAGE10

This is a list of pathogenic ClinVar variants found in the GAGE10 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-49304864-G-A		not specified	Uncertain significance (Jun 11, 2021)
X-49304887-C-T		not specified	Uncertain significance (Dec 28, 2023)
X-49304890-C-C		not specified	Likely benign (Jul 11, 2023)
X-49304895-A-G			Likely benign (Feb 01, 2023)
X-49304903-G-G		not specified	Likely benign (Oct 05, 2023)
X-49304909-T-C		not specified	Uncertain significance (Feb 15, 2023)
X-49304939-T-G		not specified	Uncertain significance (Mar 29, 2023)
X-49305448-A-T		not specified	Uncertain significance (Feb 16, 2023)
X-49305452-G-A		not specified	Uncertain significance (Dec 10, 2024)
X-49305467-C-T		not specified	Likely benign (Jun 04, 2024)
X-49305485-G-T		not specified	Uncertain significance (Apr 24, 2023)
X-49305491-G-A		not specified	Uncertain significance (Nov 21, 2023)
X-49317196-T-A		not specified	Uncertain significance (Sep 04, 2024)
X-49317196-T-G		not specified	Uncertain significance (Sep 17, 2021)
X-49317204-A-C		not specified	Uncertain significance (Oct 19, 2024)
X-49317211-G-T		not specified	Uncertain significance (Feb 05, 2024)
X-49317234-G-C		not specified	Uncertain significance (Apr 11, 2023)
X-49317256-C-G		not specified	Uncertain significance (Jun 17, 2024)
X-49317261-C-A		not specified	Uncertain significance (Aug 12, 2024)
X-49319728-G-A		not specified	Uncertain significance (Oct 04, 2024)
X-49319736-C-A		not specified	Uncertain significance (Aug 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAGE10	protein_coding	protein_coding	ENST00000407599	4	16176

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00166	0.478	125223	1	0	125224	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.928	55	38.8	1.42	0.00000294	743
Missense in Polyphen		20	13.182	1.5172		278
Synonymous	-0.990	17	12.5	1.36	9.11e-7	212
Loss of Function	0.0216	4	4.05	0.988	3.29e-7	73

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)	0.0000122	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.713
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.57

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000468

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Low	Low	Low