MS4A13

Chr 11

membrane spanning 4-domains A13

NCBI Gene: 503497 ENSG00000204979 UniProt: Q96JA4

The protein is predicted to function as a component of multimeric receptor complexes involved in cell surface signaling at the plasma membrane. This gene is extremely tolerant to loss-of-function variants (pLI near 0, LOEUF 1.6), and no established human disease associations have been reported for MS4A13 mutations. Currently, this gene lacks sufficient evidence linking it to pediatric neurological disorders.

ResearchSummary from RefSeq, UniProt

Predicted to be involved in cell surface receptor signaling pathway. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.60

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.60LOEUF

pLI 0.000

Z-score 0.32

OE 0.88 (0.50–1.60)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.14Z-score

OE missense 0.96 (0.79–1.16)

72 obs / 75.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.88 (0.50–1.60)

0≤0.351.4

Missense OE?0.96 (0.79–1.16)

0≤0.61.4

Synonymous OE?1.09

0≤1.21.6

LoF obs/exp: 7 / 8.0Missense obs/exp: 72 / 75.3Syn Z: -0.34

Background carrier burden — how many people carry a rare variant somewhere in MS4A13?

gnomAD v4 · ~730k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 290

184 rare PASS variants

Rare truncating (LoF)

1 in 2,300

50 rare PASS variants

Rare synonymous (reference)

1 in 1,600

67 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for MS4A13. 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)	~555k	1 in 350	1 in 2,900
South Asian	~43k	1 in 290	1 in 3,800
Remaining (unassigned)	~30k	1 in 230	1 in 4,300
European (Finnish)	~27k	1 in 440	≈ 1 in 13,000
Admixed American	~22k	1 in 420	1 in 3,200
African / African American	~21k	1 in 150	1 in 2,900
East Asian	~20k	1 in 660	1 in 1,200
Ashkenazi Jewish	~13k	1 in 1,600	none seen
Middle Eastern	~2,880	≈ 1 in 940	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): 2 of 5 coding exons well covered in gnomAD exomes; exons 4, 5, 6 marginal. Genomes: all 5.? see exons ↓