MS4A12

protein-coding

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

Gene summary

The protein encoded by this gene is a cell surface protein found primarily in the apical membrane of colonocytes. Silencing of this gene in colon cancer cells inhibits the proliferation, cell motility, and chemotactic invasion of cells. This gene is part of a cluster of similar genes found on chromosome 11. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]

MANE transcript

NM_017716.3

Inheritance

—

ClinVar variants

U:43B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.17

Max pathogenic AF

—

Genomic locus

chr11:60,492,778-60,507,430

External References & Databases

Ensembl (ENSG00000071203)

Transcript & Mutation Effects

hg38 • Region Span ~14.7 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MS4A12 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 47

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017716.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			43 clinvar	4 clinvar		47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)					1 clinvar	1
Total	0	0	43	5	1	49

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017716.3	RefSeq	NP_060186.2	6	MANE Select
ENST00000016913.8	Ensembl	ENSP00000016913.4	6	MANE Select
NM_001164470.2	RefSeq	NP_001157942.1	5	Standard
ENST00000526784.5	Ensembl	ENSP00000431959.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000016913
Coding exons: 6
Length: 14653
Individuals with no LoFs: 124840
Homozygous LoFs: 23
Heterozygous LoFs: 883
Defined: 125746
p: 0.00361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.119	152	148	1.03	0.00000726	1742
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.046	0.045	notable
Latino/Admixed American	0.0036	0.0036	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00032	0.00032	rare
South Asian	0.000099	0.000098	rare
Other	0.0035	0.0033	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 2.22e-16

Gene Damage Prediction

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