MS4A10

Chr 11

membrane spanning 4-domains A10

Also known as: CD20L7, MS4A9

NCBI Gene: 341116 ENSG00000172689 UniProt: Q96PG2 OMIM: 608403

The protein is a potential component of multimeric receptor complexes involved in signal transduction, containing four transmembrane domains with cytoplasmic N- and C-terminal regions. MS4A10 mutations have not been definitively associated with human disease based on current evidence. The gene shows minimal constraint against loss-of-function variants (very low pLI score), suggesting that complete loss of function may be tolerated.

OMIM ResearchSummary from RefSeq, UniProt

Most MS4A genes, including MS4A10, encode proteins with at least 4 potential transmembrane domains and N- and C-terminal cytoplasmic domains encoded by distinct exons.[supplied by OMIM, Apr 2004]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.82

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.82LOEUF

pLI 0.000

Z-score -0.83

OE 1.26 (0.84–1.82)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.19Z-score

OE missense 1.04 (0.91–1.19)

153 obs / 146.6 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.26 (0.84–1.82)

0≤0.351.4

Missense OE?1.04 (0.91–1.19)

0≤0.61.4

Synonymous OE?1.24

0≤1.21.6

LoF obs/exp: 15 / 11.9Missense obs/exp: 153 / 146.6Syn Z: -1.51

Background carrier burden — how many people carry a rare variant somewhere in MS4A10?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 160

362 rare PASS variants

Rare truncating (LoF)

1 in 1,800

68 rare PASS variants

Rare synonymous (reference)

1 in 210

146 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for MS4A10. 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 210	1 in 2,400
South Asian	~43k	1 in 110	1 in 360
Remaining (unassigned)	~30k	1 in 150	1 in 2,000
European (Finnish)	~27k	1 in 890	≈ 1 in 27,000
Admixed American	~22k	1 in 110	1 in 700
African / African American	~21k	1 in 140	1 in 4,000
East Asian	~20k	1 in 180	≈ 1 in 4,900
Ashkenazi Jewish	~13k	1 in 810	1 in 1,000
Middle Eastern	~2,884	1 in 130	≈ 1 in 2,900

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 7 coding exons well covered in gnomAD exomes; exons 6, 8 marginal. Genomes: all 7.? see exons ↓