PDS5B

PDS5 cohesin associated factor B, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 13:32586452-32778019

Previous symbols: [ "APRIN" ]

Links

ENSG00000083642 ∙ NCBI:23047 ∙ OMIM:605333 ∙ HGNC:20418 ∙ Uniprot:Q9NTI5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 25.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_015032.4	NP_055847.1	34	yes	-
ENST00000315596.15	ENSP00000313851.10	34	yes	-
ENST00000450460.5	ENSP00000401619.1	32	-	-
ENST00000447833.1	ENSP00000407005.1	6	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDS5B gene.

• not_specified (116 variants)
• not_provided (5 variants)
• PDS5B-related_developmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDS5B gene is commonly pathogenic or not. These statistics are base on transcript: NM_015032.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	2	5
missense			123		1	124
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7			7
Total	0	0	130	3	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDS5B	protein_coding	protein_coding	ENST00000315596	34	191594

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124709	0	52	124761	0.000208

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.39	404	740	0.546	0.0000374	9525
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000300	0.000298
Ashkenazi Jewish	0.00	0.00
East Asian	0.000194	0.000167
Finnish	0.000100	0.0000928
European (Non-Finnish)	0.000242	0.000212
Middle Eastern	0.000194	0.000167
South Asian	0.000609	0.000490
Other	0.000222	0.000165

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Establishment of Sister Chromatid Cohesion;S Phase;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;Cohesin Loading onto Chromatin;Mitotic Telophase/Cytokinesis;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.132
• rvis_EVS: -1.48
• rvis_percentile_EVS: 3.64

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.849

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: lens development in camera-type eye;DNA repair;mitotic sister chromatid cohesion;cell population proliferation;negative regulation of cell population proliferation;regulation of cell population proliferation;enteric nervous system development;cell division;neuroblast migration
• Cellular component: chromosome, centromeric region;chromatin;nucleus;nucleoplasm;chromosome;cytosol
• Molecular function: DNA binding;protein binding;ATP binding