MS4A6E

protein-coding

membrane spanning 4-domains A6E, the group of Membrane spanning 4-domains

Gene summary

This gene encodes a member of the membrane-spanning 4A gene family. Members of this nascent protein family are characterized by common structural features and similar intron/exon splice boundaries and display unique expression patterns among hematopoietic cells and nonlymphoid tissues. The gene encoding this protein is localized to 11q12.3, among a cluster of family members. [provided by RefSeq, Jul 2008]

MANE transcript

NM_139249.4

Inheritance

—

ClinVar variants

U:20B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr11:60,327,255-60,396,596

External References & Databases

Ensembl (ENSG00000166926)

Transcript & Mutation Effects

hg38 • Region Span ~69.3 kb

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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 MS4A6E variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 23

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_139249.4. 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 clinvar		2
missense			19 clinvar	4 clinvar		23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	20	5	0	25

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_139249.4	RefSeq	NP_640342.1	3	MANE Select
ENST00000684409.1	Ensembl	ENSP00000507799.1	3	MANE Select
ENST00000300182.8	Ensembl	ENSP00000300182.4	3	Standard
ENST00000300182.9	Ensembl	ENSP00000300182.4	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000300182
Coding exons: 3
Length: 61766
Individuals with no LoFs: 125699
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125723
p: 0.0000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.504	89	76.6	1.16	0.00000371	937
Missense (PolyPhen)		14	21.192	0.66062		303
Synonymous	-0.674	36	31.2	1.15	0.00000163	308
Loss of Function	1.10	3	5.87	0.511	2.48e-7	74

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0019	0.0011	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.000065	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0389

Intolerance Scores

LoFtool: 0.667
RVIS EVS: 0.44
RVIS percentile EVS: 77.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.165

Gene Damage Prediction

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