SSBP3

Chr 1

single stranded DNA binding protein 3

Also known as: CSDP, SSDP, SSDP1

NCBI Gene: 23648ENSG00000157216UniProt: Q9BWW4OMIM: 607390

The protein binds single-stranded DNA and acts as a transcription coactivator, particularly involved in regulating alpha 2(I) collagen gene expression and hematopoietic progenitor cell differentiation. Mutations cause autosomal dominant developmental disorders, though the specific phenotypic spectrum is still being defined. This gene is highly constrained against loss-of-function variants in the general population, suggesting mutations are likely to have significant clinical consequences.

OMIMResearchSummary from RefSeq, UniProt
LOFmechanismLOEUF 0.20
Clinical Summary— SSBP3
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
13 unique Pathogenic / Likely Pathogenic· 47 VUS of 91 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.20LOEUF
pLI 1.000
Z-score 4.90
OE 0.06 (0.03–0.20)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
2.75Z-score
OE missense 0.50 (0.43–0.58)
117 obs / 235.9 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.06 (0.03–0.20)
0≤0.351.4
Missense OE0.50 (0.43–0.58)
0≤0.61.4
Synonymous OE1.17
0≤1.21.6
LoF obs/exp: 2 / 31.9Missense obs/exp: 117 / 235.9Syn Z: -1.32
DN
0.4289th %ile
GOF
0.2995th %ile
LOF
0.83top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.20

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

91 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic10
Likely Pathogenic3
VUS47
Likely Benign2
10
Pathogenic
3
Likely Pathogenic
47
VUS
2
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
10
0
10
Likely Pathogenic
0
0
3
0
3
VUS
3
38
6
0
47
Likely Benign
0
0
0
2
2
Benign
0
0
0
0
0
Total33819262

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

View in ClinVar →

Protein Context — Lollipop Plot

SSBP3 · 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 2 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