SSX1

Chr XX-linked

SSX family member 1

Also known as: CT5.1, SPGFX5, SSRC

NCBI Gene: 6756ENSG00000126752UniProt: Q16384OMIM: 312820

SSX1 encodes a transcriptional repressor that plays a role in spermatogenesis. Mutations cause X-linked spermatogenic failure, and the gene is also involved in somatic synovial sarcoma through chromosomal translocations. The gene follows X-linked inheritance and shows very low constraint to loss-of-function variants.

OMIMResearchSummary from RefSeq, OMIM, UniProt
DNmechanismX-linkedLOEUF 2.002 OMIM phenotypes
Clinical Summary— SSX1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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ClinVar Variants
56 unique Pathogenic / Likely Pathogenic· 52 VUS of 133 total submissions
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
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
2.00LOEUF
pLI 0.000
Z-score -13.41
OE 6.50 (1.83–2.00)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-4.37Z-score
OE missense 2.45 (1.86–2.00)
176 obs / 71.7 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE6.50 (1.83–2.00)
0≤0.351.4
Missense OE2.45 (1.86–2.00)
0≤0.61.4
Synonymous OE1.14
0≤1.21.6
LoF obs/exp: 45 / 6.9Missense obs/exp: 176 / 71.7Syn Z: -0.57
DN
0.6744th %ile
GOF
0.6052th %ile
LOF
0.3164th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction 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

133 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic55
Likely Pathogenic1
VUS52
Likely Benign12
Conflicting1
55
Pathogenic
1
Likely Pathogenic
52
VUS
12
Likely Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
2
1
52
0
55
Likely Pathogenic
0
0
1
0
1
VUS
1
43
8
0
52
Likely Benign
1
7
3
1
12
Benign
0
0
0
0
0
Conflicting
—1
Total451641121

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

View in ClinVar →

Protein Context — Lollipop Plot

SSX1 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold
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
SSX1 and TRIM58 expression stratifies lung squamous cell carcinoma by tumor immune microenvironment characteristics and informs potential immunotherapy responsiveness.
Zhao X et al.·Clin Transl Oncol
2026
EWSR1::SSX1 Fusion-Driven Synovial Sarcoma: A Case Presentation and Review of the Literature.
Vega-Gonzalez J et al.·Genes Chromosomes Cancer
2025Review
Poorly differentiated biphasic synovial sarcoma of the vulva, displaying SS18::SSX1 fusion and weak to absent (mosaic) INI1/SMARCB1 immunostaining: A rare case with literature review.
Rekhi B et al.·Indian J Pathol Microbiol
2024Review
Higher Expression Levels of SSX1 and SSX2 in Patients with Colon Cancer: Regulated In Vitro by the Inhibition of Methylation and Histone Deacetylation.
Alrubie TM et al.·Medicina (Kaunas)
2023Open AccessCohort
The inhibitory effect of KIAA1456 on the proliferation and metastasis of epithelial ovarian cancer through SSX1 and AKT signaling pathway.
Zhang Y et al.·J Cancer
2023Open 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