MS4A4A

membrane spanning 4-domains A4A, the group of Membrane spanning 4-domains

Basic information

Region (hg38): 11:60185656-60318080

Previous symbols: [ "MS4A4" ]

Links

ENSG00000110079 ∙ NCBI:51338 ∙ OMIM:606547 ∙ HGNC:13371 ∙ Uniprot:Q96JQ5 ∙ 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 MS4A4A gene.

• Inborn genetic diseases (11 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MS4A4A 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			12		1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	1

Variants in MS4A4A

This is a list of pathogenic ClinVar variants found in the MS4A4A region.

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

Position	Type	Phenotype	Significance	ClinVar
11-60292301-C-A		not specified	Uncertain significance (Jan 17, 2024)
11-60292370-C-A		not specified	Uncertain significance (May 25, 2022)
11-60297207-T-C		not specified	Uncertain significance (Jun 24, 2022)
11-60297263-A-G		not specified	Uncertain significance (Jul 06, 2021)
11-60297290-G-A		not specified	Uncertain significance (Aug 13, 2021)
11-60297299-G-A		not specified	Uncertain significance (Aug 09, 2021)
11-60301026-T-C		not specified	Uncertain significance (Dec 21, 2022)
11-60301047-C-T		not specified	Uncertain significance (Oct 03, 2022)
11-60302599-T-C		not specified	Uncertain significance (Oct 27, 2022)
11-60302674-A-G		not specified	Uncertain significance (Nov 01, 2022)
11-60302703-A-G			Benign (Feb 18, 2020)
11-60306103-C-A		not specified	Likely benign (Oct 25, 2023)
11-60306104-T-C		not specified	Uncertain significance (Oct 25, 2023)
11-60306188-G-A		Inborn genetic diseases	Uncertain significance (Dec 17, 2021)
11-60306194-C-A		not specified	Uncertain significance (Jan 26, 2023)
11-60317935-A-G			Uncertain significance (Aug 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MS4A4A	protein_coding	protein_coding	ENST00000337908	7	28432

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000810	0.529	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.249	118	126	0.938	0.00000570	1543
Missense in Polyphen		18	23.512	0.76556		329
Synonymous	0.298	42	44.5	0.943	0.00000216	468
Loss of Function	0.705	9	11.6	0.777	5.71e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000162	0.000156
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.000272	0.000272
South Asian	0.00	0.00
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0563

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.0381
• hipred: N
• hipred_score: 0.112
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.133

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ms4a4a

Gene ontology

• Cellular component: integral component of membrane