TSNAX

Chr 1

translin associated factor X

Also known as: C3PO, TRAX

NCBI Gene: 7257ENSG00000116918UniProt: Q99598

This gene encodes a protein which specifically interacts with translin, a DNA-binding protein that binds consensus sequences at breakpoint junctions of chromosomal translocations. The encoded protein contains bipartite nuclear targeting sequences that may provide nuclear transport for translin, which lacks any nuclear targeting motifs. [provided by RefSeq, Jul 2008]

78
ClinVar variants
38
Pathogenic / LP
0.49
pLI score
1
Active trials
Clinical Summary— TSNAX
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.20) despite low pLI — interpret in context.
📋
ClinVar Variants
38 Pathogenic / Likely Pathogenic· 32 VUS of 78 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

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.
0.53LOEUF
pLI 0.489
Z-score 2.82
OE 0.20 (0.09–0.53)
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.
1.30Z-score
OE missense 0.70 (0.60–0.82)
107 obs / 152.2 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 (0.09–0.53)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.70 (0.60–0.82)
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.1.06
0≤1.21.6
LoF obs/exp: 3 / 14.7Missense obs/exp: 107 / 152.2Syn Z: -0.33

ClinVar Variant Classifications

78 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic35
Likely Pathogenic3
VUS32
Benign4
35
Pathogenic
3
Likely Pathogenic
32
VUS
4
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
35
0
35
Likely Pathogenic
0
0
3
0
3
VUS
0
28
4
0
32
Likely Benign
0
0
0
0
0
Benign
0
1
1
2
4
Total02943274

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

View in ClinVar →

Protein Context — Lollipop Plot

TSNAX · 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
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
The associations between cognitive functions and TSNAX genetic variations in patients with schizophrenia.
Huang KY et al.·Pharmacol Biochem Behav
2023Cohort
Translin-associated factor X gene (TSNAX) may be associated with female major depressive disorder in the Japanese population.
Okuda A et al.·Neuromolecular Med
2010
Sofosbuvir induces gene expression for promoting cell proliferation and migration of hepatocellular carcinoma cells.
Tsai WL et al.·Aging (Albany NY)
2022
Chronic Periodontitis Genome-wide Association Study in the Hispanic Community Health Study / Study of Latinos.
Sanders AE et al.·J Dent Res
2017
Association of distinct allelic haplotypes of DISC1 with psychotic and bipolar spectrum disorders and with underlying cognitive impairments.
Palo OM et al.·Hum Mol Genet
2007
DISC1 splice variants are upregulated in schizophrenia and associated with risk polymorphisms.
Nakata K et al.·Proc Natl Acad Sci U S A
2009
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
Blast Phase Chronic Myeloid Leukemia, BCR-ABL1 PositiveRecurrent Acute Lymphoblastic LeukemiaRecurrent Chronic Lymphocytic Leukemia

Anti-CD19/20/22 Chimeric Antigen Receptor T Cells (TriCAR19.20.22 T Cells) for the Treatment of Relapsed or Refractory Non-Hodgkin Lymphoma, Acute Lymphoblastic Leukemia, and Chronic Lymphocytic Leukemia

RECRUITING
NCT07166419Phase PHASE1Ohio State University Comprehensive Cancer CenterStarted 2026-02-01
Autologous Anti-CD19/CD20/CD22 CAR T-cellsBiospecimen CollectionBone Marrow Aspiration

External Resources

Links to major genomics databases and tools