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]

81
ClinVar variants
28
Pathogenic / LP
0.71
pLI score
0
Active trials
Clinical Summary— SNX9
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.71) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
28 Pathogenic / Likely Pathogenic· 48 VUS of 81 total submissions
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?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
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?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.82Z-score
OE missense 0.72 (0.65–0.80)
237 obs / 330.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.20 (0.12–0.37)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.72 (0.65–0.80)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.83
0≤1.21.6
LoF obs/exp: 8 / 39.2Missense obs/exp: 237 / 330.2Syn Z: 1.42

ClinVar Variant Classifications

81 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic26
Likely Pathogenic2
VUS48
Likely Benign4
Benign1
26
Pathogenic
2
Likely Pathogenic
48
VUS
4
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
26
0
26
Likely Pathogenic
0
0
2
0
2
VUS
0
46
2
0
48
Likely Benign
0
2
1
1
4
Benign
0
0
1
0
1
Total04832181

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in 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.

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Genome-Wide Association Approach Identified Novel Genetic Predictors of Heart Rate Response to β-Blockers.
Shahin MH et al.·J Am Heart Assoc
2018Meta-analysis
An overview of CDK3 in cancer: clinical significance and pharmacological implications.
Teo T et al.·Pharmacol Res
2022Review
Tight junctions and enteropathogenic E. coli.
Weflen AW et al.·Ann N Y Acad Sci
2009
Screening for host proteins interacting with Escherichia coli O157:H7 EspF using bimolecular fluorescence complementation.
Hua Y et al.·Future Microbiol
2018
Therapy-related acute myeloid leukemia with KMT2A-SNX9 gene fusion associated with a hyperdiploid karyotype after hemophagocytic lymphohistiocytosis.
Sardou-Cezar I et al.·Cancer Genet
2021Case report
Identification of a cancer-associated fibroblast classifier for predicting prognosis and therapeutic response in lung squamous cell carcinoma.
Lai X et al.·Medicine (Baltimore)
2023
A pan-cancer study of ADAM9's immunological function and prognostic value particularly in liver cancer.
AmeliMojarad M et al.·Sci Rep
2024
A single chlamydial protein reshapes the plasma membrane and serves as recruiting platform for central endocytic effector proteins.
Spona D et al.·Commun Biol
2023
The landscape of fusion transcripts in spitzoid melanoma and biologically indeterminate spitzoid tumors by RNA sequencing.
Wu G et al.·Mod Pathol
2016
Genetic risk factors for severe and fatigue dominant long COVID and commonalities with ME/CFS identified by combinatorial analysis.
Taylor K et al.·J Transl Med
2023
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

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