STX3

Chr 11AR

syntaxin 3

Also known as: DIAR12, MVID2, RDMVID, STX3A

NCBI Gene: 6809 ENSG00000166900 UniProt: Q13277 OMIM: 600876

The gene is a member of the syntaxin family. The encoded protein is targeted to the apical membrane of epithelial cells where it forms clusters and is important in establishing and maintaining polarity necessary for protein trafficking involving vesicle fusion and exocytosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

OMIM Research

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Diarrhea 12, with microvillus atrophyMIM #619445

Retinal dystrophy and microvillus inclusion diseaseMIM #619446

Clinical highlights

Gene–disease validity

Not independently assessedOMIM lists Diarrhea 12, with microvillus atrophy; Retinal dystrophy and microvillus inclusion disease; no ClinGen or GenCC tier

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

—

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 STX3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 87

491 rare PASS variants

Rare truncating (LoF)

1 in 1,700

69 rare PASS variants

Rare synonymous (reference)

1 in 390

154 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for STX3. 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 1,600
South Asian	~43k	1 in 100	1 in 1,300
Remaining (unassigned)	~30k	1 in 140	1 in 2,400
European (Finnish)	~27k	1 in 240	≈ 1 in 5,900
Admixed American	~22k	1 in 130	≈ 1 in 5,600
African / African American	~21k	1 in 140	1 in 1,100
East Asian	~20k	1 in 100	1 in 1,700
Ashkenazi Jewish	~13k	1 in 460	none seen
Middle Eastern	~2,884	1 in 88	≈ 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.