VSTM5

Chr 11

V-set and transmembrane domain containing 5

Also known as: C11orf90

NCBI Gene: 387804 ENSG00000214376 UniProt: A8MXK1 OMIM: 621118

Predicted to be involved in several processes, including filopodium assembly; positive regulation of excitatory synapse assembly; and protein homooligomerization. Predicted to be located in membrane. Predicted to be active in axon; dendrite; and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.85

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.85LOEUF

pLI 0.000

Z-score -0.59

OE 1.22 (0.74–1.85)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.98Z-score

OE missense 0.74 (0.62–0.89)

83 obs / 112.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.22 (0.74–1.85)

0≤0.351.4

Missense OE?0.74 (0.62–0.89)

0≤0.61.4

Synonymous OE?0.96

0≤1.21.6

LoF obs/exp: 10 / 8.2Missense obs/exp: 83 / 112.2Syn Z: 0.19

Background carrier burden — how many people carry a rare variant somewhere in VSTM5?

gnomAD v4 · ~700k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 170

236 rare PASS variants

Rare truncating (LoF)

1 in 1,100

52 rare PASS variants

Rare synonymous (reference)

1 in 300

107 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for VSTM5. 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)	~540k	1 in 290	1 in 1,000
South Asian	~40k	1 in 290	1 in 1,700
Remaining (unassigned)	~29k	1 in 130	1 in 1,200
European (Finnish)	~25k	1 in 700	1 in 4,900
African / African American	~21k	1 in 140	1 in 1,700
East Asian	~18k	1 in 330	1 in 1,600
Admixed American	~18k	1 in 87	1 in 850
Ashkenazi Jewish	~13k	≈ 1 in 3,100	none seen
Middle Eastern	~2,852	1 in 150	≈ 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): All 4 coding exons well covered in gnomAD exomes and genomes.? see exons ↓