SNX10

Chr 7AR

sorting nexin 10

Also known as: OPTB8

NCBI Gene: 29887ENSG00000086300UniProt: Q9Y5X0OMIM: 614780

This gene encodes a phosphoinositide-binding protein that regulates protein sorting and membrane trafficking in endosomes, and is required for cilium biogenesis and osteoclast differentiation. SNX10 mutations cause autosomal recessive osteopetrosis, a bone disorder characterized by defective bone resorption leading to increased bone density and fractures. The gene shows low constraint against loss-of-function variants (high LOEUF score), consistent with its recessive inheritance pattern.

OMIMResearchSummary from RefSeq, OMIM, UniProt
GOFmechanismARLOEUF 1.661 OMIM phenotype
Clinical Summary— SNX10
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Gene-Disease Validity (ClinGen)
autosomal recessive osteopetrosis 8 · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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ClinVar Variants
54 unique Pathogenic / Likely Pathogenic· 75 VUS of 207 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.66LOEUF
pLI 0.000
Z-score -0.25
OE 1.07 (0.71–1.66)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.55Z-score
OE missense 0.85 (0.72–1.01)
95 obs / 111.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE1.07 (0.71–1.66)
0≤0.351.4
Missense OE0.85 (0.72–1.01)
0≤0.61.4
Synonymous OE0.89
0≤1.21.6
LoF obs/exp: 14 / 13.0Missense obs/exp: 95 / 111.2Syn Z: 0.54
DN
0.5870th %ile
GOF
0.6345th %ile
LOF
0.3163th %ile

The highest-scoring mechanism for this gene is gain-of-function.

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

207 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic39
Likely Pathogenic15
VUS75
Likely Benign60
Benign15
Conflicting1
39
Pathogenic
15
Likely Pathogenic
75
VUS
60
Likely Benign
15
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
10
1
28
0
39
Likely Pathogenic
9
1
5
0
15
VUS
3
58
14
0
75
Likely Benign
0
1
32
27
60
Benign
0
1
11
3
15
Conflicting
—1
Total22629030205

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

View in ClinVar →

Protein Context — Lollipop Plot

SNX10 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
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
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