SNX10

Chr 7AR

sorting nexin 10

Also known as: OPTB8

NCBI Gene: 29887ENSG00000086300UniProt: Q9Y5X0

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 some family members. This gene may play a role in regulating endosome homeostasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2010]

Primary Disease Associations & Inheritance

Osteopetrosis, autosomal recessive 8MIM #615085
AR
205
ClinVar variants
54
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— SNX10
🧬
Gene-Disease Validity (ClinGen)
autosomal recessive osteopetrosis 8 · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
54 Pathogenic / Likely Pathogenic· 75 VUS of 205 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
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.
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?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.
0.55Z-score
OE missense 0.85 (0.72–1.01)
95 obs / 111.2 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.1.07 (0.71–1.66)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.85 (0.72–1.01)
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.0.89
0≤1.21.6
LoF obs/exp: 14 / 13.0Missense obs/exp: 95 / 111.2Syn Z: 0.54

ClinVar Variant Classifications

205 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
3
1
35
0
39
Likely Pathogenic
6
1
8
0
15
VUS
1
57
17
0
75
Likely Benign
0
1
32
27
60
Benign
0
1
11
3
15
Conflicting
—1
Total106110330205

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.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
SORTING NEXIN 10; SNX10
MIM #614780 · *

Osteopetrosis, autosomal recessive 8

MIM #615085

Molecular basis of disorder known

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Sorting Nexin 10 Mediates Metabolic Reprogramming of Macrophages in Atherosclerosis Through the Lyn-Dependent TFEB Signaling Pathway.
You Y et al.·Circ Res
2020
Fusion of Tumor Cells with Lipid-Associated Macrophages Drives Metastatic Progression of Breast Cancer.
Cheng Y et al.·Cancer Res
2026
Sorting nexin 10 regulates lysosomal ionic homeostasis via ClC-7 by controlling PI(3,5)P2.
Wu JZ et al.·J Cell Biol
2025
Inhibiting SNX10 induces autophagy to suppress invasion and EMT and inhibits the PI3K/AKT pathway in cervical cancer.
Liao D et al.·Clin Transl Oncol
2025
SNX10 gene mutation in infantile malignant osteopetrosis: A case report and literature review.
Zhou T et al.·Zhong Nan Da Xue Xue Bao Yi Xue Ban
2021Review
SNX10 regulates the proliferation, apoptosis and cell cycle of acute B lymphoblastic leukemia cells via the PI3K/Akt signaling pathway.
Wang C et al.·Oncol Rep
2025
Ropivacaine inhibits the proliferation and metastasis of gastric cancer cells via the SNX10/SRC/STAT3 pathway.
Deng RR et al.·Chem Biol Drug Des
2024
Sorting nexin 10 sustains PDGF receptor signaling in glioblastoma stem cells via endosomal protein sorting.
Gimple RC et al.·JCI Insight
2023
The molecular structure and function of sorting nexin 10 in skeletal disorders, cancers, and other pathological conditions.
Xu J et al.·J Cell Physiol
2021Review
Differential transcriptomic host responses in the early phase of viral and bacterial infections in human lung tissue explants ex vivo.
Sohail A et al.·Respir Res
2024
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