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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			61		1	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	61	1	3

Variants in PDS5B

This is a list of pathogenic ClinVar variants found in the PDS5B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
13-32648789-C-A		not specified	Uncertain significance (Jan 15, 2025)
13-32658239-G-T		PDS5B-related developmental disorder	Uncertain significance (Jul 11, 2023)
13-32659206-A-G		not specified	Uncertain significance (Aug 30, 2021)
13-32667769-A-C		not specified	Uncertain significance (Jun 26, 2023)
13-32675849-T-C			Benign (Jun 19, 2018)
13-32675944-A-C		not specified	Uncertain significance (Jun 29, 2022)
13-32687158-A-C		not specified	Uncertain significance (Mar 23, 2023)
13-32687254-C-T		not specified	Uncertain significance (Nov 18, 2022)
13-32687255-A-G		not specified	Uncertain significance (May 16, 2022)
13-32688469-C-T		not specified	Uncertain significance (Feb 05, 2025)
13-32688511-A-G			Benign (Jul 02, 2018)
13-32688528-C-G		not specified	Uncertain significance (Dec 09, 2023)
13-32694273-A-G		not specified	Uncertain significance (Jan 26, 2022)
13-32699834-C-G		not specified	Uncertain significance (Feb 22, 2023)
13-32699855-G-T		not specified	Uncertain significance (Jan 06, 2023)
13-32699856-C-T		not specified	Uncertain significance (Oct 12, 2024)
13-32701428-G-A		not specified	Uncertain significance (Jan 18, 2023)
13-32706974-G-A		not specified	Uncertain significance (May 18, 2023)
13-32709999-A-G			Likely benign (Mar 01, 2023)
13-32710086-G-C		not specified	Uncertain significance (Aug 28, 2024)
13-32732103-C-T		not specified	Uncertain significance (May 25, 2023)
13-32732148-G-A		not specified	Uncertain significance (Mar 07, 2025)
13-32732198-G-A		not specified	Uncertain significance (Feb 21, 2024)
13-32735179-A-T		not specified	Uncertain significance (Jul 17, 2023)
13-32735184-A-T		not specified	Uncertain significance (Feb 16, 2023)

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
1.00	9.13e-8	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

Haploinsufficiency Scores

• pHI: 0.544
• hipred: Y
• hipred_score: 0.696
• ghis: 0.684

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

Mouse Genome Informatics

• Gene name: Pds5b
• Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; skeleton phenotype; embryo phenotype; respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; vision/eye phenotype

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