SNX2

Chr 5

sorting nexin 2

Also known as: TRG-9

NCBI Gene: 6643ENSG00000205302UniProt: O60749

This gene belongs to the sorting nexin family whose members contain the phosphoinositide-binding phox (PX) domain. The encoded protein is a component of the retromer complex which plays a role in protein sorting in the endocytic pathway. This protein may form oligomeric complexes with other family members. Alternate splicing results in multiple transcript variants of this gene. Pseudogenes associated with this gene are located on chromosomes 1 and 7. [provided by RefSeq, May 2013]

0
Active trials
21
Pathogenic / LP
87
ClinVar variants
7
Pubs (1 yr)
0.6
Missense Z
0.30
LOEUF· LoF intolerant
Clinical Summary— SNX2
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.98). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
21 Pathogenic / Likely Pathogenic· 65 VUS of 87 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.30LOEUF
pLI 0.985
Z-score 4.43
OE 0.13 (0.06–0.30)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
0.60Z-score
OE missense 0.90 (0.81–1.00)
238 obs / 265.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.13 (0.06–0.30)
0≤0.351.4
Missense OE0.90 (0.81–1.00)
0≤0.61.4
Synonymous OE1.07
0≤1.21.6
LoF obs/exp: 4 / 30.3Missense obs/exp: 238 / 265.3Syn Z: -0.50

ClinVar Variant Classifications

87 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic21
VUS65
Likely Benign1
21
Pathogenic
65
VUS
1
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
21
0
21
Likely Pathogenic
0
0
0
0
0
VUS
0
55
10
0
65
Likely Benign
0
0
1
0
1
Benign
0
0
0
0
0
Total05532087

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

View in ClinVar →

SNX2 · 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 →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Enhancing the electrocatalytic performance of SnX2 (X = S and Se) monolayers for CO2 reduction to HCOOH via transition metal atom adsorption: a theoretical investigation.
Xia F et al.·RSC Adv
2023Open Access
Canonical and Non-Canonical Roles of SNX1 and SNX2 in Endosomal Membrane Dynamics.
Da Graça J et al.·Contact (Thousand Oaks)
2023Open Access
A SNX1-SNX2-VAPB partnership regulates endosomal membrane rewiring in response to nutritional stress.
Da Graça J et al.·Life Sci Alliance
2023Open Access
Cancer-associated fibroblast-derived exosome miR-181b-3p promotes the occurrence and development of colorectal cancer by regulating SNX2 expression.
Jiang Y et al.·Biochem Biophys Res Commun
2023
Strain tunable magnetism in SnX2 (X = S, Se) monolayers by hole doping.
Xiang H et al.·Sci Rep
2016Open Access
Top 5 resultsSearch Europe PMC ↗

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