SNX9

Chr 6

sorting nexin 9

Also known as: SDP1, SH3PX1, SH3PXD3A, WISP

NCBI Gene: 51429ENSG00000130340UniProt: Q9Y5X1

This gene encodes a member of the sorting nexin family. Members of this family contain a phosphoinositide binding domain, and are involved in intracellular trafficking. The encoded protein does not contain a coiled coil region, like some family members, but does contain a SRC homology domain near its N-terminus. The encoded protein is reported to have a variety of interaction partners, including of adaptor protein 2 , dynamin, tyrosine kinase non-receptor 2, Wiskott-Aldrich syndrome-like, and ARP3 actin-related protein 3. The encoded protein is implicated in several stages of intracellular trafficking, including endocytosis, macropinocytosis, and F-actin nucleation. [provided by RefSeq, Jul 2013]

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
0
Active trials
19
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.37
LOEUF
—
Mechanism
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?
0.37LOEUF
pLI 0.706
Z-score 4.62
OE 0.20 (0.12–0.37)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
1.82Z-score
OE missense 0.72 (0.65–0.80)
237 obs / 330.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.20 (0.12–0.37)
0≤0.351.4
Missense OE?0.72 (0.65–0.80)
0≤0.61.4
Synonymous OE?0.83
0≤1.21.6
LoF obs/exp: 8 / 39.2Missense obs/exp: 237 / 330.2Syn Z: 1.42

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

SNX9 · 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