MS4A6A

membrane spanning 4-domains A6A, the group of Membrane spanning 4-domains

Basic information

Region (hg38): 11:60172014-60184666

Previous symbols: [ "MS4A6" ]

Links

ENSG00000110077 ∙ NCBI:64231 ∙ OMIM:606548 ∙ HGNC:13375 ∙ Uniprot:Q9H2W1 ∙ 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 MS4A6A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MS4A6A 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			7	2		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	0

Variants in MS4A6A

This is a list of pathogenic ClinVar variants found in the MS4A6A region.

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

Position	Type	Phenotype	Significance	ClinVar
11-60173071-G-A		not specified	Likely benign (Oct 02, 2023)
11-60175517-G-T		not specified	Uncertain significance (Feb 27, 2024)
11-60179838-G-C		not specified	Uncertain significance (May 26, 2022)
11-60179856-G-A		not specified	Uncertain significance (Mar 23, 2022)
11-60179951-C-A		not specified	Uncertain significance (Jan 26, 2022)
11-60181619-G-T		not specified	Uncertain significance (Jun 18, 2021)
11-60181620-G-T		not specified	Uncertain significance (Oct 17, 2023)
11-60181691-C-T		not specified	Uncertain significance (Nov 08, 2021)
11-60181697-T-C		not specified	Likely benign (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MS4A6A	protein_coding	protein_coding	ENST00000412309	6	13059

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.38e-13	0.00281	125279	2	463	125744	0.00185

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.457	144	129	1.11	0.00000609	1625
Missense in Polyphen		35	30.948	1.1309		440
Synonymous	-0.381	56	52.5	1.07	0.00000260	528
Loss of Function	-1.84	15	9.04	1.66	3.78e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000999	0.000999
Ashkenazi Jewish	0.000695	0.000695
East Asian	0.00305	0.00299
Finnish	0.00434	0.00431
European (Non-Finnish)	0.00233	0.00233
Middle Eastern	0.00305	0.00299
South Asian	0.0000980	0.0000980
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0823

Intolerance Scores

• loftool: 0.946
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.0718
• hipred: N
• hipred_score: 0.112
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00858

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ms4a6d

Gene ontology

• Cellular component: integral component of membrane