MS4A12

membrane spanning 4-domains A12, the group of Membrane spanning 4-domains

Basic information

Region (hg38): 11:60492778-60507430

Links

ENSG00000071203 ∙ NCBI:54860 ∙ OMIM:606550 ∙ HGNC:13370 ∙ Uniprot:Q9NXJ0 ∙ 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 MS4A12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MS4A12 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				1		1
missense			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	18	3	1

Variants in MS4A12

This is a list of pathogenic ClinVar variants found in the MS4A12 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-60497324-G-T		not specified	Uncertain significance (Oct 03, 2023)
11-60497325-T-C		not specified	Uncertain significance (Feb 27, 2024)
11-60497379-C-A		not specified	Uncertain significance (Aug 12, 2021)
11-60497460-C-T		not specified	Uncertain significance (Jun 09, 2022)
11-60497461-G-A		not specified	Uncertain significance (Jul 09, 2021)
11-60497482-C-T		not specified	Uncertain significance (Oct 26, 2022)
11-60497483-A-G			Likely benign (Jul 01, 2020)
11-60497527-T-C		not specified	Likely benign (Aug 21, 2023)
11-60497559-G-A		not specified	Uncertain significance (Jan 04, 2024)
11-60497570-T-G		not specified	Uncertain significance (Jun 02, 2024)
11-60497586-G-T		not specified	Uncertain significance (Jun 02, 2024)
11-60501082-T-C		not specified	Uncertain significance (May 16, 2024)
11-60501118-G-A		not specified	Uncertain significance (Dec 22, 2023)
11-60501133-T-A		not specified	Uncertain significance (Dec 20, 2023)
11-60502032-G-A		not specified	Uncertain significance (May 16, 2024)
11-60503700-G-T			Benign (Jun 10, 2018)
11-60503708-G-A		not specified	Uncertain significance (Feb 13, 2024)
11-60503728-G-A		not specified	Uncertain significance (Nov 09, 2023)
11-60503770-G-A		not specified	Uncertain significance (Aug 02, 2022)
11-60506753-C-T		not specified	Likely benign (Apr 04, 2023)
11-60506819-C-T		not specified	Uncertain significance (Dec 21, 2022)
11-60507051-G-C		not specified	Uncertain significance (Nov 01, 2022)
11-60507063-C-T		not specified	Uncertain significance (Jan 26, 2023)
11-60507084-C-T		not specified	Uncertain significance (Jun 17, 2024)
11-60507114-C-A		not specified	Uncertain significance (Dec 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MS4A12	protein_coding	protein_coding	ENST00000016913	6	14653

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.50e-9	0.0524	124840	23	883	125746	0.00361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.119	152	148	1.03	0.00000726	1742
Missense in Polyphen		30	31.911	0.94012		434
Synonymous	0.723	44	50.5	0.871	0.00000257	536
Loss of Function	-0.496	12	10.3	1.17	4.36e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0494	0.0489
Ashkenazi Jewish	0.000301	0.000298
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000319	0.000316
Middle Eastern	0.00	0.00
South Asian	0.0000994	0.0000980
Other	0.00348	0.00326

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0488

Intolerance Scores

• loftool: 0.949
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• pHI: 0.0219
• 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: 2.22e-16

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ms4a12

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding