PDCD5

programmed cell death 5

Basic information

Region (hg38): 19:32581190-32587453

Links

ENSG00000105185 ∙ NCBI:9141 ∙ OMIM:604583 ∙ HGNC:8764 ∙ Uniprot:O14737 ∙ 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 PDCD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDCD5 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						0
missense			10		1	11
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	10	0	1

Variants in PDCD5

This is a list of pathogenic ClinVar variants found in the PDCD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-32581277-C-T		not specified	Uncertain significance (Jul 16, 2024)
19-32581289-A-G		not specified	Uncertain significance (Apr 15, 2024)
19-32581307-G-A			Benign (Dec 14, 2017)
19-32581311-T-C		not specified	Uncertain significance (Mar 01, 2025)
19-32582208-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-32584943-G-A			Benign (Dec 14, 2017)
19-32585002-C-T		not specified	Uncertain significance (Jul 26, 2022)
19-32585003-G-A		not specified	Uncertain significance (Dec 03, 2021)
19-32585870-T-G		not specified	Uncertain significance (Oct 17, 2023)
19-32586876-A-G		not specified	Uncertain significance (Apr 04, 2023)
19-32586901-A-G		not specified	Uncertain significance (Dec 05, 2024)
19-32586914-G-T		not specified	Uncertain significance (Mar 06, 2025)
19-32587272-T-C		not specified	Uncertain significance (Jun 28, 2022)
19-32587286-G-T		not specified	Uncertain significance (Apr 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDCD5	protein_coding	protein_coding	ENST00000590247	6	6385

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00364	0.856	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.298	56	62.6	0.894	0.00000300	814
Missense in Polyphen		12	14.773	0.81232		220
Synonymous	0.707	17	21.1	0.804	0.00000116	211
Loss of Function	1.24	5	9.00	0.556	3.80e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.000203	0.000198
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function in the process of apoptosis.

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.353
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.520
• hipred: Y
• hipred_score: 0.842
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdcd5

Gene ontology

• Biological process: apoptotic process;negative regulation of cell population proliferation;positive regulation of gene expression;positive regulation of apoptotic process;positive regulation of cysteine-type endopeptidase activity involved in apoptotic process;cellular response to transforming growth factor beta stimulus;positive regulation of release of cytochrome c from mitochondria;positive regulation of protein import into mitochondrial outer membrane;negative regulation of chaperone-mediated protein folding
• Cellular component: nucleus;cytoplasm;cytosol;extracellular exosome
• Molecular function: DNA binding;protein binding;heparin binding;acetyltransferase activator activity;beta-tubulin binding