PDCD4

programmed cell death 4, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 10:110871794-110900006

Links

ENSG00000150593 ∙ NCBI:27250 ∙ OMIM:608610 ∙ HGNC:8763 ∙ Uniprot:Q53EL6 ∙ 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 PDCD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDCD4 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					2	2
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	2

Variants in PDCD4

This is a list of pathogenic ClinVar variants found in the PDCD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-110881291-G-A			Benign (Jun 06, 2018)
10-110881394-C-T		not specified	Uncertain significance (Oct 25, 2022)
10-110881416-C-T		not specified	Uncertain significance (Dec 13, 2021)
10-110881428-G-T		not specified	Uncertain significance (Jan 26, 2023)
10-110881439-G-A		not specified	Uncertain significance (May 04, 2022)
10-110883009-C-T		not specified	Uncertain significance (Jun 07, 2023)
10-110885317-C-A		not specified	Uncertain significance (Mar 30, 2024)
10-110885328-C-A		not specified	Uncertain significance (May 20, 2024)
10-110887670-G-A		not specified	Uncertain significance (Apr 07, 2022)
10-110887846-A-T		not specified	Uncertain significance (Mar 14, 2023)
10-110889623-C-G		not specified	Uncertain significance (Jan 04, 2024)
10-110890623-T-G		not specified	Uncertain significance (Apr 23, 2024)
10-110890645-A-G		not specified	Uncertain significance (Dec 01, 2022)
10-110894099-G-C		not specified	Uncertain significance (Dec 22, 2023)
10-110894119-T-C		not specified	Uncertain significance (Feb 13, 2024)
10-110894182-A-G		not specified	Uncertain significance (Oct 13, 2023)
10-110894445-A-G		not specified	Uncertain significance (Jan 19, 2024)
10-110894480-C-T			Benign (May 21, 2018)
10-110895964-A-G		not specified	Uncertain significance (Jul 05, 2023)
10-110896009-C-G		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDCD4	protein_coding	protein_coding	ENST00000280154	11	28200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.36e-7	0.938	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.218	239	249	0.961	0.0000123	3063
Missense in Polyphen		77	94.509	0.81474		1158
Synonymous	-0.177	92	89.9	1.02	0.00000467	891
Loss of Function	1.83	14	23.6	0.593	0.00000116	318

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000403	0.000397
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000165	0.000163
South Asian	0.000215	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits translation initiation and cap-dependent translation. May excert its function by hindering the interaction between EIF4A1 and EIF4G. Inhibits the helicase activity of EIF4A. Modulates the activation of JUN kinase. Down-regulates the expression of MAP4K1, thus inhibiting events important in driving invasion, namely, MAPK85 activation and consequent JUN-dependent transcription. May play a role in apoptosis. Tumor suppressor. Inhibits tumor promoter-induced neoplastic transformation. Binds RNA (By similarity). {ECO:0000250, ECO:0000269|PubMed:16357133, ECO:0000269|PubMed:16449643, ECO:0000269|PubMed:17053147, ECO:0000269|PubMed:18296639, ECO:0000269|PubMed:19153607, ECO:0000269|PubMed:19204291}.
• Pathway: Proteoglycans in cancer - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;Interferon type I signaling pathways;mTOR signaling pathway (Consensus)

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.943
• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.06

Haploinsufficiency Scores

• pHI: 0.613
• hipred: Y
• hipred_score: 0.703
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.877

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdcd4
• 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); reproductive system phenotype; neoplasm; immune system phenotype; renal/urinary system phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: pdcd4b
• Affected structure: atrioventricular valve
• Phenotype tag: abnormal
• Phenotype quality: constricted

Gene ontology

• Biological process: apoptotic process;cell aging;BMP signaling pathway;interleukin-12-mediated signaling pathway;negative regulation of apoptotic process;negative regulation of JUN kinase activity;negative regulation of cell cycle;negative regulation of transcription, DNA-templated;positive regulation of inflammatory response;epithelial to mesenchymal transition involved in cardiac fibroblast development;cellular response to lipopolysaccharide;negative regulation of cytokine production involved in inflammatory response;positive regulation of NIK/NF-kappaB signaling;negative regulation of vascular smooth muscle cell proliferation;negative regulation of myofibroblast differentiation;negative regulation of vascular smooth muscle cell differentiation;positive regulation of vascular associated smooth muscle cell apoptotic process;positive regulation of endothelial cell apoptotic process
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: RNA binding;protein binding