MS4A5

membrane spanning 4-domains A5, the group of Membrane spanning 4-domains

Basic information

Region (hg38): 11:60429572-60455214

Links

ENSG00000166930 ∙ NCBI:64232 ∙ OMIM:606499 ∙ HGNC:13374 ∙ Uniprot:Q9H3V2 ∙ 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 MS4A5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MS4A5 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in MS4A5

This is a list of pathogenic ClinVar variants found in the MS4A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-60429690-G-A		not specified	Uncertain significance (May 13, 2024)
11-60429693-C-T		not specified	Uncertain significance (Mar 14, 2024)
11-60429699-C-T		not specified	Uncertain significance (Dec 30, 2024)
11-60429738-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-60429777-A-T		not specified	Likely benign (Jul 02, 2024)
11-60429785-C-G		not specified	Uncertain significance (Jul 16, 2024)
11-60430809-T-C		not specified	Uncertain significance (Mar 07, 2023)
11-60430877-T-C		not specified	Uncertain significance (Nov 28, 2023)
11-60430907-T-C		not specified	Uncertain significance (Nov 03, 2023)
11-60430914-G-T		not specified	Uncertain significance (Jan 03, 2025)
11-60432426-G-A		not specified	Uncertain significance (Mar 01, 2024)
11-60432439-C-G		not specified	Uncertain significance (Nov 06, 2023)
11-60432456-A-G		not specified	Uncertain significance (Nov 03, 2023)
11-60433778-G-A		not specified	Uncertain significance (Feb 05, 2024)
11-60433849-G-A		not specified	Uncertain significance (Nov 08, 2021)
11-60447736-T-C		not specified	Uncertain significance (May 06, 2022)
11-60447740-A-G		not specified	Uncertain significance (Mar 08, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MS4A5	protein_coding	protein_coding	ENST00000300190	5	25626

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000379	0.639	125699	0	8	125707	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0935	95	97.6	0.973	0.00000433	1291
Missense in Polyphen		25	23.455	1.0659		332
Synonymous	0.713	30	35.4	0.848	0.00000173	378
Loss of Function	0.695	6	8.14	0.737	4.27e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000469	0.0000469
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000765	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0840

Intolerance Scores

• loftool: 0.722
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.23

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0980

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ms4a5

Gene ontology

• Cellular component: integral component of membrane