MS4A10

membrane spanning 4-domains A10, the group of Membrane spanning 4-domains

Basic information

Region (hg38): 11:60785333-60801305

Links

ENSG00000172689 ∙ NCBI:341116 ∙ OMIM:608403 ∙ HGNC:13368 ∙ Uniprot:Q96PG2 ∙ 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 MS4A10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MS4A10 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			9	1		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	9	1	0

Variants in MS4A10

This is a list of pathogenic ClinVar variants found in the MS4A10 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-60790367-G-A		not specified	Likely benign (Jan 30, 2024)
11-60790442-C-T		not specified	Uncertain significance (May 11, 2022)
11-60790516-G-C		not specified	Uncertain significance (Jun 11, 2024)
11-60790992-G-A		not specified	Uncertain significance (Apr 19, 2024)
11-60791023-T-C		not specified	Uncertain significance (Apr 25, 2022)
11-60791043-C-A		not specified	Uncertain significance (May 27, 2022)
11-60791047-A-G		not specified	Uncertain significance (Jan 30, 2024)
11-60794027-T-C		not specified	Uncertain significance (Sep 14, 2022)
11-60794043-G-T		not specified	Uncertain significance (May 26, 2022)
11-60794068-G-A		not specified	Uncertain significance (Mar 01, 2023)
11-60798418-C-T		not specified	Uncertain significance (Oct 12, 2022)
11-60798487-G-A		not specified	Uncertain significance (Dec 08, 2021)
11-60799862-T-C		not specified	Uncertain significance (May 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MS4A10	protein_coding	protein_coding	ENST00000308287	7	15958

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.14e-11	0.0130	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.187	153	147	1.04	0.00000770	1730
Missense in Polyphen		39	39.394	0.99		529
Synonymous	-1.51	78	62.8	1.24	0.00000382	537
Loss of Function	-0.828	15	11.9	1.26	5.07e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000162	0.000152
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000553	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.000588	0.000588
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0685

Intolerance Scores

• loftool: 0.877
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.0454
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0357

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ms4a10

Gene ontology

• Cellular component: integral component of membrane