MS4A15

membrane spanning 4-domains A15, the group of Membrane spanning 4-domains

Basic information

Region (hg38): 11:60756867-60776733

Links

ENSG00000166961 ∙ NCBI:219995 ∙ ∙ HGNC:28573 ∙ Uniprot:Q8N5U1 ∙ 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 MS4A15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MS4A15 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			30	1		31
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	1	0

Variants in MS4A15

This is a list of pathogenic ClinVar variants found in the MS4A15 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-60763740-G-C		not specified	Uncertain significance (Dec 30, 2024)
11-60763749-G-A		not specified	Likely benign (Jan 24, 2025)
11-60763759-G-A		not specified	Uncertain significance (May 24, 2023)
11-60763787-C-G		not specified	Uncertain significance (Oct 07, 2024)
11-60763788-G-A		not specified	Uncertain significance (Oct 04, 2022)
11-60763789-C-A		not specified	Uncertain significance (Mar 11, 2024)
11-60763824-A-G		not specified	Uncertain significance (Apr 06, 2023)
11-60763842-C-T		not specified	Uncertain significance (May 04, 2022)
11-60763891-G-A		not specified	Uncertain significance (Jan 20, 2023)
11-60763915-G-T		not specified	Uncertain significance (Aug 20, 2023)
11-60763939-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-60767534-C-T		not specified	Uncertain significance (Nov 12, 2024)
11-60767551-G-C		not specified	Uncertain significance (Mar 30, 2024)
11-60767597-G-A		not specified	Uncertain significance (Apr 08, 2022)
11-60767628-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
11-60767636-C-A		not specified	Uncertain significance (Mar 13, 2023)
11-60771307-C-T		not specified	Uncertain significance (Aug 09, 2021)
11-60771319-C-T		not specified	Uncertain significance (Aug 08, 2023)
11-60773422-A-G		not specified	Uncertain significance (Nov 06, 2023)
11-60773429-T-G		not specified	Uncertain significance (May 23, 2023)
11-60773430-G-T		not specified	Uncertain significance (Feb 26, 2025)
11-60773435-C-T		not specified	Uncertain significance (Jan 04, 2022)
11-60773462-T-A		not specified	Uncertain significance (Sep 26, 2024)
11-60773470-G-A		not specified	Uncertain significance (Nov 18, 2022)
11-60773482-C-T		not specified	Likely benign (Dec 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MS4A15	protein_coding	protein_coding	ENST00000405633	6	19780

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000443	0.673	125708	1	39	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.233	138	146	0.946	0.00000810	1551
Missense in Polyphen		37	42.993	0.86061		504
Synonymous	-0.654	68	61.5	1.11	0.00000406	509
Loss of Function	0.772	6	8.42	0.713	4.14e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.00	0.00
South Asian	0.000457	0.000425
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.582
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.53

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.172

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.377

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ms4a15

Gene ontology

• Cellular component: integral component of membrane