MS4A3

Chr 11

membrane spanning 4-domains A3

Also known as: CD20L, HTM4

NCBI Gene: 932 ENSG00000149516 UniProt: Q96HJ5 OMIM: 606498

This gene encodes a member of the membrane-spanning 4A gene family. Members of this 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. This family member likely plays a role in signal transduction and may function as a subunit associated with receptor complexes. The gene encoding this protein is localized to 11q12, among a cluster of related family members. Alternative splicing may result in multiple transcript variants; however, not all variants have been fully described. [provided by RefSeq, Jul 2008]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

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P/LP missense

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LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

gnomad: Error: gnomAD API error: 400

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

Background carrier burden — how many people carry a rare variant somewhere in MS4A3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 140

298 rare PASS variants

Rare truncating (LoF)

1 in 2,900

56 rare PASS variants

Rare synonymous (reference)

1 in 350

89 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for MS4A3. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 160	1 in 3,800
South Asian	~43k	1 in 130	1 in 1,100
Remaining (unassigned)	~30k	1 in 140	1 in 790
European (Finnish)	~27k	1 in 810	1 in 4,400
Admixed American	~22k	1 in 180	1 in 1,000
African / African American	~21k	1 in 210	1 in 3,200
East Asian	~20k	1 in 110	≈ 1 in 9,900
Ashkenazi Jewish	~13k	1 in 760	none seen
Middle Eastern	~2,884	1 in 220	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 5 of 6 coding exons well covered in gnomAD exomes; exon 7 marginal. Genomes: all 6.? see exons ↓