MAGEA4

MAGE family member A4, the group of MAGE family

Basic information

Region (hg38): X:151912495-151925171

Previous symbols: [ "MAGE4" ]

Links

ENSG00000147381 ∙ NCBI:4103 ∙ OMIM:300175 ∙ HGNC:6802 ∙ Uniprot:P43358 ∙ 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 MAGEA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGEA4 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				4		4
missense			30	6		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	10	0

Variants in MAGEA4

This is a list of pathogenic ClinVar variants found in the MAGEA4 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-151923719-C-G		not specified	Uncertain significance (Jun 26, 2024)
X-151923837-A-G		not specified	Likely benign (Sep 03, 2024)
X-151923867-G-A		not specified	Uncertain significance (Sep 20, 2023)
X-151923882-C-T		not specified	Uncertain significance (Aug 02, 2021)
X-151923895-C-T			Likely benign (Apr 01, 2023)
X-151923918-A-G		not specified	Uncertain significance (Jul 27, 2024)
X-151923932-A-G		not specified	Uncertain significance (Dec 21, 2022)
X-151923950-C-T		not specified	Uncertain significance (Jul 27, 2022)
X-151923952-A-G			Likely benign (Feb 01, 2023)
X-151923960-C-G		not specified	Uncertain significance (Jan 29, 2025)
X-151923960-C-T		not specified	Uncertain significance (Jun 29, 2022)
X-151924031-C-T		not specified	Uncertain significance (Nov 22, 2024)
X-151924041-G-A		not specified	Uncertain significance (Sep 17, 2021)
X-151924087-C-G		not specified	Uncertain significance (Nov 09, 2024)
X-151924100-C-T		not specified	Uncertain significance (Dec 17, 2024)
X-151924113-T-A		not specified	Uncertain significance (Apr 24, 2024)
X-151924132-C-T			Likely benign (Mar 01, 2022)
X-151924163-G-T		not specified	Uncertain significance (Mar 17, 2023)
X-151924199-C-G		not specified	Uncertain significance (Oct 27, 2023)
X-151924215-G-A		not specified	Uncertain significance (Jun 29, 2023)
X-151924238-G-T		not specified	Uncertain significance (Dec 20, 2023)
X-151924245-A-G		not specified	Uncertain significance (Oct 20, 2024)
X-151924277-A-G		not specified	Uncertain significance (Mar 25, 2024)
X-151924313-G-A		not specified	Uncertain significance (Jan 11, 2023)
X-151924355-G-T		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGEA4	protein_coding	protein_coding	ENST00000360243	1	12662

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	-1.54	174	126	1.39	0.00000969	2040
Missense in Polyphen		30	31.682	0.9469		638
Synonymous	-2.24	74	53.2	1.39	0.00000419	671
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: Not known, though may play a role in embryonal development and tumor transformation or aspects of tumor progression.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.340
• rvis_EVS: 1.06
• rvis_percentile_EVS: 91.58

Haploinsufficiency Scores

• pHI: 0.0838
• hipred: N
• hipred_score: 0.337

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.325

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