PDCD5

protein-coding

programmed cell death 5

Gene summary

This gene encodes a protein that is upregulated during apoptosis where it translocates rapidly from the cytoplasm to the nucleus. The encoded protein may be an important regulator of K(lysine) acetyltransferase 5 (a protein involved in transcription, DNA damage response and cell cycle control) by inhibiting its proteasome-dependent degradation. Pseudogenes have been identified on chromosomes 5 and 12 [provided by RefSeq, Dec 2010]

MANE transcript

NM_004708.4

Inheritance

—

ClinVar variants

U:20B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr19:32,581,190-32,587,453

External References & Databases

Ensembl (ENSG00000105185)

Transcript & Mutation Effects

hg38 • Region Span ~6.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PDCD5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 14

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004708.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			16 clinvar		1 clinvar	17
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	20	0	1	21

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004708.4	RefSeq	NP_004699.1	6	MANE Select
ENST00000590247.7	Ensembl	ENSP00000466214.1	6	MANE Select
ENST00000221784.8	Ensembl	ENSP00000221784.4	4	Standard
ENST00000379316.3	Ensembl	ENSP00000368620.3	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

DNA binding
protein binding
heparin binding
acetyltransferase activator activity
beta-tubulin binding

Cellular Component

nucleus
cytoplasm
cytosol
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000590247
Coding exons: 6
Length: 6385
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125748
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.298	56	62.6	0.894	0.00000300	814
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.981

Gene Damage Prediction

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