MS4A13

membrane spanning 4-domains A13, the group of Membrane spanning 4-domains

Basic information

Region (hg38): 11:60515392-60542721

Links

ENSG00000204979 ∙ NCBI:503497 ∙ ∙ HGNC:16674 ∙ Uniprot:Q5J8X5 ∙ 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 MS4A13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MS4A13 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			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in MS4A13

This is a list of pathogenic ClinVar variants found in the MS4A13 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-60518130-T-C		not specified	Uncertain significance (Feb 09, 2025)
11-60518154-C-G		not specified	Uncertain significance (Sep 14, 2023)
11-60523946-G-A		not specified	Likely benign (Jan 02, 2024)
11-60529380-G-A		not specified	Uncertain significance (Aug 21, 2023)
11-60529387-G-T		not specified	Uncertain significance (May 31, 2023)
11-60529405-A-G		not specified	Uncertain significance (Jan 08, 2024)
11-60529417-T-C		not specified	Uncertain significance (Apr 01, 2024)
11-60529434-C-T		not specified	Likely benign (May 16, 2024)
11-60529436-C-G		not specified	Uncertain significance (May 17, 2023)
11-60529459-T-C		not specified	Uncertain significance (Feb 24, 2025)
11-60542530-A-C		not specified	Uncertain significance (Mar 31, 2023)
11-60542541-C-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MS4A13	protein_coding	protein_coding	ENST00000378186	5	27309

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000462	0.430	125587	0	8	125595	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.136	72	75.3	0.956	0.00000372	969
Missense in Polyphen		24	23.585	1.0176		329
Synonymous	-0.339	27	24.9	1.09	0.00000117	298
Loss of Function	0.322	7	7.98	0.877	3.98e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000644	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000365	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000712	0.0000655
Other	0.000183	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in signal transduction as a component of a multimeric receptor complex. {ECO:0000250}.

Intolerance Scores

• loftool: 0.891
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.58

Haploinsufficiency Scores

• pHI: 0.0254
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00361

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ms4a13
• Phenotype: normal phenotype

Gene ontology

• Cellular component: integral component of membrane