MAGEA6

MAGE family member A6, the group of MAGE family

Basic information

Region (hg38): X:152766136-152769716

Previous symbols: [ "MAGE6" ]

Links

ENSG00000197172 ∙ NCBI:4105 ∙ OMIM:300176 ∙ HGNC:6804 ∙ Uniprot:P43360 ∙ 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 MAGEA6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGEA6 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			22	2	3	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	3

Variants in MAGEA6

This is a list of pathogenic ClinVar variants found in the MAGEA6 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-152766735-C-T		not specified	Uncertain significance (Feb 15, 2023)
X-152766767-C-T		not specified	Uncertain significance (May 15, 2023)
X-152766771-T-C			Likely benign (Feb 01, 2024)
X-152766774-T-G		not specified	Uncertain significance (Oct 10, 2023)
X-152766787-G-C		not specified	Uncertain significance (Jul 17, 2023)
X-152766795-C-T		not specified	Uncertain significance (Mar 30, 2024)
X-152766801-C-T		not specified	Uncertain significance (Nov 10, 2022)
X-152766838-G-C		not specified	Uncertain significance (Oct 31, 2023)
X-152766900-C-T		not specified	Uncertain significance (Dec 19, 2022)
X-152766912-T-A		not specified	Uncertain significance (Mar 21, 2024)
X-152766934-G-C		not specified	Likely benign (Aug 30, 2021)
X-152766939-T-G		not specified	Uncertain significance (Jun 05, 2024)
X-152766968-A-G		not specified	Uncertain significance (Dec 22, 2023)
X-152767002-G-A		not specified	Uncertain significance (May 26, 2024)
X-152767019-T-C			Benign (Jun 11, 2018)
X-152767058-T-C			Benign (Jun 22, 2018)
X-152767101-G-C		not specified	Uncertain significance (Dec 28, 2023)
X-152767130-T-A		not specified	Uncertain significance (Jan 08, 2024)
X-152767184-T-C		not specified	Uncertain significance (Feb 14, 2024)
X-152767230-C-T			Likely benign (May 02, 2018)
X-152767233-C-G		not specified	Uncertain significance (Mar 21, 2024)
X-152767233-C-T		not specified	Uncertain significance (Oct 06, 2021)
X-152767248-T-C		not specified	Uncertain significance (Feb 07, 2023)
X-152767296-A-G		not specified	Uncertain significance (Jan 18, 2023)
X-152767308-T-C			Benign (Jun 11, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGEA6	protein_coding	protein_coding	ENST00000329342	1	3612

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-4.36	233	106	2.19	0.00000824	2042
Missense in Polyphen		45	25.577	1.7594		614
Synonymous	-5.22	92	46.6	1.97	0.00000404	639
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proposed to enhance ubiquitin ligase activity of RING- type zinc finger-containing E3 ubiquitin-protein ligases. May enhance ubiquitin ligase activity of TRIM28 and stimulate p53/TP53 ubiquitination by TRIM28. Proposed to act through recruitment and/or stabilization of the Ubl-conjugating enzyme (E2) at the E3:substrate complex. May play a role in tumor transformation or aspects of tumor progression. In vitro promotes cell viability in melanoma cell lines. {ECO:0000269|PubMed:17942928, ECO:0000269|PubMed:20864041}.

Intolerance Scores

• loftool: 0.363
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.74

Haploinsufficiency Scores

• pHI: 0.0385
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0167

Gene Damage Prediction

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

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function;protein binding