PDS5B

Chr 13

PDS5 cohesin associated factor B

Also known as: APRIN, AS3, CG008

NCBI Gene: 23047ENSG00000083642UniProt: Q9NTI5OMIM: 605333

The PDS5B protein regulates sister chromatid cohesion during mitosis by stabilizing the cohesin complex's association with chromatin, ensuring accurate chromosome segregation. Mutations cause Cornelia de Lange syndrome with autosomal dominant inheritance, characterized by intellectual disability, growth restriction, limb malformations, and distinctive facial features. This gene is highly constrained against loss-of-function variants, reflecting its essential role in chromosome biology.

OMIMResearchSummary from RefSeq, UniProt
LOFmechanismLOEUF 0.18
Clinical Summary— PDS5B
⚡
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
45 unique Pathogenic / Likely Pathogenic· 122 VUS of 210 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint
0.18LOEUF
pLI 1.000
Z-score 7.47
OE 0.10 (0.06–0.18)
Highly constrained

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

Missense Constraint
4.39Z-score
OE missense 0.55 (0.50–0.59)
404 obs / 740.4 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios
LoF OE0.10 (0.06–0.18)
0≤0.351.4
Missense OE0.55 (0.50–0.59)
0≤0.61.4
Synonymous OE1.02
0≤1.21.6
LoF obs/exp: 8 / 80.2Missense obs/exp: 404 / 740.4Syn Z: -0.23
DN
0.2997th %ile
GOF
0.3292th %ile
LOF
0.77top 5%

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

LOFprediction above median · LOEUF 0.18

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

210 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic45
VUS122
Likely Benign3
Benign3
45
Pathogenic
122
VUS
3
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
45
0
45
Likely Pathogenic
0
0
0
0
0
VUS
0
116
6
0
122
Likely Benign
0
0
0
3
3
Benign
0
1
0
2
3
Total0117515173

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

View in ClinVar →

Protein Context — Lollipop Plot

PDS5B · 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 4 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
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