SNX3

Chr 6

sorting nexin 3

Also known as: Grd19, MCOPS8, SDP3

NCBI Gene: 8724ENSG00000112335UniProt: O60493

This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region, like most family members. This protein interacts with phosphatidylinositol-3-phosphate, and is involved in protein trafficking. A pseudogene of this gene is present on the sex chromosomes. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
0
Active trials
16
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.84
LOEUF
LOF
Mechanism· G2P
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
0.84LOEUF
pLI 0.249
Z-score 1.86
OE 0.27 (0.11–0.84)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
1.73Z-score
OE missense 0.49 (0.38–0.63)
44 obs / 90.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.27 (0.11–0.84)
0≤0.351.4
Missense OE?0.49 (0.38–0.63)
0≤0.61.4
Synonymous OE?1.24
0≤1.21.6
LoF obs/exp: 2 / 7.5Missense obs/exp: 44 / 90.1Syn Z: -1.13

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

SNX3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients