PDS5A

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

Basic information

Region (hg38): 4:39822863-39977956

Links

ENSG00000121892 ∙ NCBI:23244 ∙ OMIM:613200 ∙ HGNC:29088 ∙ Uniprot:Q29RF7 ∙ 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 PDS5A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDS5A 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		1
missense			40	1		41
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	42	2	0

Variants in PDS5A

This is a list of pathogenic ClinVar variants found in the PDS5A region.

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

Position	Type	Phenotype	Significance	ClinVar
4-39838008-A-C		not specified	Uncertain significance (Jul 25, 2023)
4-39838037-C-G		not specified	Uncertain significance (May 16, 2023)
4-39838039-G-C		not specified	Uncertain significance (Sep 22, 2023)
4-39838108-G-C		not specified	Uncertain significance (Apr 26, 2023)
4-39844695-A-C		not specified	Uncertain significance (Jan 20, 2025)
4-39844720-T-C		not specified	Likely benign (Apr 15, 2024)
4-39844774-C-T		not specified	Uncertain significance (Sep 19, 2022)
4-39844779-C-T		not specified	Uncertain significance (Jan 28, 2025)
4-39844800-G-A		not specified	Uncertain significance (May 25, 2022)
4-39848909-T-C		not specified	Uncertain significance (Aug 21, 2023)
4-39848930-T-C		not specified	Uncertain significance (Jan 10, 2022)
4-39848939-C-T		not specified	Uncertain significance (Dec 13, 2023)
4-39848942-A-C		not specified	Uncertain significance (May 16, 2023)
4-39849596-G-T		not specified	Uncertain significance (Dec 02, 2022)
4-39862226-T-G		not specified	Uncertain significance (Apr 08, 2024)
4-39862889-T-C		not specified	Uncertain significance (Sep 17, 2021)
4-39862939-G-C		not specified	Uncertain significance (Jan 22, 2025)
4-39863031-G-A		not specified	Uncertain significance (Jul 12, 2022)
4-39863454-G-C		not specified	Uncertain significance (Dec 07, 2022)
4-39866944-C-A		not specified	Uncertain significance (Mar 04, 2024)
4-39866946-G-A		not specified	Uncertain significance (Jul 18, 2024)
4-39866988-T-C		not specified	Uncertain significance (Jan 19, 2024)
4-39869405-C-T		not specified	Uncertain significance (May 05, 2023)
4-39869421-T-G		not specified	Uncertain significance (Dec 27, 2023)
4-39873039-T-C		not specified	Uncertain significance (Dec 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDS5A	protein_coding	protein_coding	ENST00000303538	32	155094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000220	124632	0	6	124638	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	5.05	287	649	0.442	0.0000318	8787
Missense in Polyphen		57	220.2	0.25886		3199
Synonymous	0.827	215	231	0.931	0.0000115	2463
Loss of Function	6.81	7	67.2	0.104	0.00000366	925

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000477	0.0000464
European (Non-Finnish)	0.0000356	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable 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. {ECO:0000269|PubMed:15855230, ECO:0000269|PubMed:19907496}.
• 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: 0.102

Intolerance Scores

• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.2

Haploinsufficiency Scores

• pHI: 0.684
• hipred: Y
• hipred_score: 0.765
• ghis: 0.649

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.848

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pds5a
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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); growth/size/body region phenotype; cellular phenotype; craniofacial 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); digestive/alimentary 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); 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); respiratory system phenotype; embryo phenotype; skeleton phenotype; renal/urinary system phenotype; vision/eye phenotype

Gene ontology

• Biological process: DNA repair;mitotic sister chromatid cohesion;negative regulation of DNA replication;cell division
• Cellular component: chromosome, centromeric region;chromatin;nucleus;nucleoplasm;chromosome;cytosol;plasma membrane
• Molecular function: protein binding