SSBP3

Chr 1

single stranded DNA binding protein 3

Also known as: CSDP, SSDP, SSDP1

NCBI Gene: 23648 ENSG00000157216 UniProt: Q9BWW4 OMIM: 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.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to enable single-stranded DNA binding activity and transcription coactivator activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.20

Clinical Summary— SSBP3

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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.

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ClinVar Variants

42 VUS of 73 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 OE?0.06 (0.03–0.20)

0≤0.351.4

Missense OE?0.50 (0.43–0.58)

0≤0.61.4

Synonymous OE?1.17

0≤1.21.6

LoF obs/exp: 2 / 31.9Missense obs/exp: 117 / 235.9Syn Z: -1.32

This gene — mechanism propensity

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

73 submitted variants in ClinVar

ClinVar

Classification Summary

VUS42

Likely Benign2

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	0	0	0	0
VUS	3	38	1	0	42
Likely Benign	0	0	0	2	2
Benign	0	0	0	0	0
Total	3	38	1	2	44

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

View in ClinVar →

13 pathogenic / likely-pathogenic (of 18) ClinVar copy-number / structural variants overlap SSBP3 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →