MAGEA3

MAGE family member A3, the group of MAGE family

Basic information

Region (hg38): X:152698767-152702347

Previous symbols: [ "MAGE3" ]

Links

ENSG00000221867 ∙ NCBI:4102 ∙ OMIM:300174 ∙ HGNC:6801 ∙ Uniprot:P43357 ∙ 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 MAGEA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGEA3 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					6	6
missense			27	5	2	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	5	8

Variants in MAGEA3

This is a list of pathogenic ClinVar variants found in the MAGEA3 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-152700915-C-T		not specified	Uncertain significance (Jan 26, 2022)
X-152700932-G-C		not specified	Uncertain significance (Nov 05, 2021)
X-152700974-G-C		not specified	Uncertain significance (Mar 08, 2025)
X-152701003-G-C		not specified	Uncertain significance (Oct 04, 2024)
X-152701021-G-C		not specified	Uncertain significance (Oct 04, 2024)
X-152701038-C-A		not specified	Uncertain significance (Jul 09, 2021)
X-152701141-C-T			Benign/Likely benign (Mar 01, 2025)
X-152701143-A-G		not specified	Likely benign (Jul 25, 2023)
X-152701161-G-A		not specified	Uncertain significance (Sep 25, 2024)
X-152701168-G-C		not specified	Uncertain significance (Dec 17, 2023)
X-152701175-G-A			Likely benign (Jan 22, 2018)
X-152701181-G-A		not specified	Uncertain significance (Jan 30, 2024)
X-152701202-T-C		not specified	Uncertain significance (Feb 13, 2025)
X-152701206-G-A		not specified	Uncertain significance (Dec 19, 2022)
X-152701250-G-A		not specified	Uncertain significance (Dec 16, 2023)
X-152701267-T-C			Benign (Jan 22, 2018)
X-152701288-C-G		not specified	Uncertain significance (Jan 21, 2025)
X-152701298-A-G			Likely benign (Jan 22, 2018)
X-152701299-G-A			Likely benign (Jan 22, 2018)
X-152701333-G-A		not specified	Uncertain significance (Jan 18, 2025)
X-152701334-G-A		not specified	Uncertain significance (Dec 07, 2024)
X-152701353-A-G		not specified	Uncertain significance (Nov 01, 2022)
X-152701444-C-T			Benign (May 08, 2018)
X-152701459-C-T			Benign (Aug 01, 2024)
X-152701529-G-A		not specified	Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGEA3	protein_coding	protein_coding	ENST00000393902	1	3589

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	-2.34	174	106	1.64	0.00000827	2040
Missense in Polyphen		30	24.716	1.2138		613
Synonymous	-4.98	90	46.7	1.93	0.00000400	643
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 embryonal development and tumor transformation or aspects of tumor progression. In vitro promotes cell viability in melanoma cell lines. Antigen recognized on a melanoma by autologous cytolytic T-lymphocytes. {ECO:0000269|PubMed:20864041}.

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.417
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.0348
• hipred: N
• hipred_score: 0.337
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.429

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of protein processing;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
• Cellular component: endoplasmic reticulum
• Molecular function: protein binding;caspase binding