PDS5B
protein-codingPDS5 cohesin associated factor B, the group of Armadillo like helical domain containing
Gene summary
This gene encodes a protein that interacts with the conserved protein complex termed cohesin. The cohesin complex holds together sister chromatids and facilitates accurate chromosome segregation during mitosis and meiosis. This protein is also a negative regulator of cell proliferation and may be a tumor-suppressor gene. [provided by RefSeq, Jul 2015]
- APRIN
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~191.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PDS5B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015032.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 2 | 5 | |||
| missense | 123 | 1 | 124 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 0 | 0 | 133 | 3 | 3 | 139 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055847.1 | 34 | MANE Select | |
| Ensembl | ENSP00000313851.10 | 34 | MANE Select | |
| Ensembl | ENSP00000407005.1 | 6 | Standard | |
| Ensembl | ENSP00000401619.1 | 32 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Establishment of Sister Chromatid Cohesion
- S Phase
- Mitotic Prometaphase
- Separation of Sister Chromatids
- Mitotic Anaphase
Biological Process
- lens development in camera-type eye
- DNA repair
- mitotic sister chromatid cohesion
- cell population proliferation
- negative regulation of cell population proliferation
Molecular Function
- DNA binding
- protein binding
- ATP binding
Cellular Component
- chromosome, centromeric region
- chromatin
- nucleus
- nucleoplasm
- chromosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000315596
- Coding exons
- 34
- Length
- 191594
- Individuals with no LoFs
- 124709
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 52
- Defined
- 124761
- p
- 0.000208
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 4.39 | 404 | 740 | 0.546 | 0.0000374 | 9525 |
| Missense (PolyPhen) | 33 | 134.63 | 0.24512 | 1719 | ||
| Synonymous | -0.228 | 253 | 248 | 1.02 | 0.0000120 | 2620 |
| Loss of Function | 7.47 | 8 | 80.2 | 0.0998 | 0.00000446 | 1032 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000067 | 0.000065 | rare |
| Latino/Admixed American | 0.00023 | 0.00017 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00019 | 0.00017 | rare |
| Finnish | 0.00010 | 0.000093 | rare |
| European (Non-Finnish) | 0.00024 | 0.00021 | rare |
| South Asian | 0.00061 | 0.00049 | rare |
| Other | 0.00022 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulator of sister chromatid cohesion in mitosis which may stabilize cohesin complex association with chromatin. May couple sister chromatid cohesion during mitosis to DNA replication. Cohesion ensures that chromosome partitioning is accurate in both meiotic and mitotic cells and plays an important role in DNA repair. Plays a role in androgen-induced proliferative arrest in prostate cells. {ECO:0000269|PubMed:10963680, ECO:0000269|PubMed:15855230, ECO:0000269|PubMed:19696148}.;
Recessive Scores
- pRec
- 0.145
Intolerance Scores
- LoFtool
- 0.132
- RVIS EVS
- -1.48
- RVIS percentile EVS
- 3.64
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.849
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |