STMN3

Chr 20

stathmin 3

Also known as: SCLIP

NCBI Gene: 50861ENSG00000197457UniProt: Q9NZ72

This gene encodes a protein which is a member of the stathmin protein family. Members of this protein family form a complex with tubulins at a ratio of 2 tubulins for each stathmin protein. Microtubules require the ordered assembly of alpha- and beta-tubulins, and formation of a complex with stathmin disrupts microtubule formation and function. A pseudogene of this gene is located on chromosome 22. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]

96
ClinVar variants
52
Pathogenic / LP
0.08
pLI score
0
Active trials
Clinical Summary— STMN3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.08) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
52 Pathogenic / Likely Pathogenic· 42 VUS of 96 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.
0.91LOEUF
pLI 0.084
Z-score 1.75
OE 0.35 (0.16–0.91)
Tolerant

Typical tolerance to LoF variation

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.
1.34Z-score
OE missense 0.63 (0.51–0.77)
65 obs / 103.4 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.0.35 (0.16–0.91)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.63 (0.51–0.77)
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.1.03
0≤1.21.6
LoF obs/exp: 3 / 8.5Missense obs/exp: 65 / 103.4Syn Z: -0.14

ClinVar Variant Classifications

96 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic44
Likely Pathogenic8
VUS42
Likely Benign1
Conflicting1
44
Pathogenic
8
Likely Pathogenic
42
VUS
1
Likely Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
44
0
44
Likely Pathogenic
0
0
8
0
8
VUS
0
22
20
0
42
Likely Benign
0
1
0
0
1
Benign
0
0
0
0
0
Conflicting
—1
Total02372096

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

View in ClinVar →

Protein Context — Lollipop Plot

STMN3 · 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
STATHMIN-LIKE 3; STMN3
MIM #608362 · *
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Relationship between genetically determined telomere length and glioma risk.
Saunders CN et al.·Neuro Oncol
2022
Identification and validation of a dysregulated TME-related gene signature for predicting prognosis, and immunological properties in bladder cancer.
Shen C et al.·Front Immunol
2023
RUNX1 Is a Driver of Renal Cell Carcinoma Correlating with Clinical Outcome.
Rooney N et al.·Cancer Res
2020
Knockdown of the psychosis susceptibility gene ZNF804A alters expression of genes involved in cell adhesion.
Hill MJ et al.·Hum Mol Genet
2012
Triangulating Molecular Evidence to Prioritize Candidate Causal Genes at Established Atopic Dermatitis Loci.
Sobczyk MK et al.·J Invest Dermatol
2021
A functional variant on 20q13.33 related to glioma risk alters enhancer activity and modulates expression of multiple genes.
Ali MW et al.·Hum Mutat
2021Functional
Predicting Survival Signature of Bladder Cancer Related to Cancer-Associated Fibroblast (CAF) Constructed by Intersecting Genes in TCGA and GEO.
Zheng K et al.·Mol Biotechnol
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