MAGEA12

MAGE family member A12, the group of MAGE family

Basic information

Region (hg38): X:152733756-152737669

Previous symbols: [ "MAGE12" ]

Links

ENSG00000213401 ∙ NCBI:4111 ∙ OMIM:300177 ∙ HGNC:6799 ∙ Uniprot:P43365 ∙ 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 MAGEA12 gene.

• Inborn genetic diseases (11 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGEA12 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			9	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	3	0

Variants in MAGEA12

This is a list of pathogenic ClinVar variants found in the MAGEA12 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-152736217-A-G		not specified	Likely benign (Oct 12, 2021)
X-152736238-T-C		not specified	Uncertain significance (Aug 14, 2023)
X-152736244-C-T		not specified	Uncertain significance (Aug 01, 2022)
X-152736410-C-T			Likely benign (Feb 01, 2023)
X-152736416-G-T		not specified	Uncertain significance (Nov 12, 2021)
X-152736504-G-C		not specified	Uncertain significance (Dec 11, 2023)
X-152736673-G-C		not specified	Likely benign (Jul 14, 2021)
X-152736678-G-A		not specified	Uncertain significance (Jul 14, 2021)
X-152736747-G-C		not specified	Uncertain significance (Oct 26, 2022)
X-152736832-A-G		not specified	Uncertain significance (Apr 28, 2023)
X-152736837-A-G		not specified	Uncertain significance (May 18, 2023)
X-152736853-C-G		not specified	Uncertain significance (Jun 29, 2022)
X-152737041-A-T		not specified	Uncertain significance (Oct 26, 2022)
X-152737054-A-G		not specified	Uncertain significance (Dec 20, 2023)
X-152737096-G-C		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGEA12	protein_coding	protein_coding	ENST00000393900	1	3892

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	-0.405	132	120	1.10	0.00000954	2031
Missense in Polyphen		8	21.326	0.37513		443
Synonymous	-4.74	96	52.4	1.83	0.00000439	641
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 tumor transformation or progression. In vitro promotes cell viability in melanoma cell lines. {ECO:0000269|PubMed:17942928}.

Recessive Scores

• pRec: 0.0677

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.0385
• hipred: N
• hipred_score: 0.158
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.946

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