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.

not_specified (103 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_000015032.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	2 clinvar	4
missense			104 clinvar		1 clinvar	105
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	104	2	3

Loading clinvar variants...

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