ENTPD5

ectonucleoside triphosphate diphosphohydrolase 5 (inactive), the group of Ectonucleoside triphosphate diphosphohydrolase family

Basic information

Region (hg38): 14:73958009-74019399

Previous symbols: [ "CD39L4", "PCPH" ]

Links

ENSG00000187097 ∙ NCBI:957 ∙ OMIM:603162 ∙ HGNC:3367 ∙ Uniprot:O75356 ∙ 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 ENTPD5 gene.

• Inborn genetic diseases (15 variants)
• not specified (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENTPD5 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	15	0	2

Variants in ENTPD5

This is a list of pathogenic ClinVar variants found in the ENTPD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-73958139-C-T			Likely benign (Aug 10, 2023)
14-73958142-C-G			Likely benign (Jan 22, 2024)
14-73958149-C-T		Familial steroid-resistant nephrotic syndrome with sensorineural deafness	Pathogenic (May 01, 2011)
14-73958150-G-A			Uncertain significance (May 21, 2022)
14-73958150-G-T		Inborn genetic diseases	Uncertain significance (Jun 22, 2023)
14-73958152-G-A			Uncertain significance (Sep 01, 2021)
14-73958158-G-A			Uncertain significance (May 21, 2022)
14-73958162-T-C			Uncertain significance (Oct 20, 2022)
14-73958163-C-T		Familial steroid-resistant nephrotic syndrome with sensorineural deafness • COQ6-related disorder	Likely benign (Oct 16, 2023)
14-73958189-C-T		Inborn genetic diseases	Uncertain significance (Jun 14, 2022)
14-73958202-A-G			Likely benign (Jul 05, 2022)
14-73958211-G-A		Inborn genetic diseases	Uncertain significance (Mar 03, 2022)
14-73958214-C-T			Likely benign (Nov 23, 2022)
14-73958215-G-A		Inborn genetic diseases	Uncertain significance (Feb 24, 2022)
14-73958219-C-G		Familial steroid-resistant nephrotic syndrome with sensorineural deafness	Uncertain significance (Dec 13, 2021)
14-73958229-G-A		Familial steroid-resistant nephrotic syndrome with sensorineural deafness	Pathogenic (Feb 25, 2022)
14-73958235-T-C		not specified • Familial steroid-resistant nephrotic syndrome with sensorineural deafness	Benign (Feb 01, 2024)
14-73958253-C-T			Likely benign (Jun 29, 2023)
14-73958256-C-T			Likely benign (Jul 01, 2023)
14-73958274-G-C			Uncertain significance (Dec 20, 2021)
14-73958275-T-C			Likely benign (Dec 13, 2023)
14-73958353-C-A			Benign (Jun 23, 2018)
14-73958966-T-C			Conflicting classifications of pathogenicity (Mar 01, 2024)
14-73958980-G-C			Uncertain significance (Jan 23, 2020)
14-73958990-A-G			Uncertain significance (Apr 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENTPD5	protein_coding	protein_coding	ENST00000334696	13	61390

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000455	0.998	125632	0	115	125747	0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.412	210	227	0.923	0.0000111	2785
Missense in Polyphen		89	101.74	0.87476		1241
Synonymous	-0.180	88	85.9	1.02	0.00000441	828
Loss of Function	2.77	12	27.7	0.433	0.00000152	303

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00282	0.00282
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000397	0.000387
Middle Eastern	0.00	0.00
South Asian	0.000653	0.000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Uridine diphosphatase (UDPase) that promotes protein N- glycosylation and ATP level regulation. UDP hydrolysis promotes protein N-glycosylation and folding in the endoplasmic reticulum, as well as elevated ATP consumption in the cytosol via an ATP hydrolysis cycle. Together with CMPK1 and AK1, constitutes an ATP hydrolysis cycle that converts ATP to AMP and results in a compensatory increase in aerobic glycolysis. The nucleotide hydrolyzing preference is GDP > IDP > UDP, but not any other nucleoside di-, mono- or triphosphates, nor thiamine pyrophosphate. Plays a key role in the AKT1-PTEN signaling pathway by promoting glycolysis in proliferating cells in response to phosphoinositide 3-kinase (PI3K) signaling. {ECO:0000269|PubMed:10400613}.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Purine Nucleoside Phosphorylase Deficiency;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Xanthine Dehydrogenase Deficiency (Xanthinuria);Adenylosuccinate Lyase Deficiency;AICA-Ribosiduria;Thioguanine Action Pathway;Adenine phosphoribosyltransferase deficiency (APRT);Mitochondrial DNA depletion syndrome;Myoadenylate deaminase deficiency;Purine Metabolism;Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Nucleobase catabolism;Metabolism of nucleotides;Phosphate bond hydrolysis by NTPDase proteins;Purine metabolism;Metabolism;Pyrimidine metabolism;Purine nucleotides nucleosides metabolism;Pyrimidine nucleotides nucleosides metabolism (Consensus)

Recessive Scores

• pRec: 0.177

Intolerance Scores

• loftool: 0.868
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.96

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.474

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Entpd5
• Phenotype: growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; liver/biliary system phenotype; neoplasm; reproductive 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); hematopoietic system phenotype

Zebrafish Information Network

• Gene name: entpd5a
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: dead

Gene ontology

• Biological process: protein N-linked glycosylation;cell population proliferation;regulation of phosphatidylinositol 3-kinase signaling;nucleobase-containing small molecule catabolic process;positive regulation of glycolytic process;ATP metabolic process;'de novo' posttranslational protein folding
• Cellular component: extracellular region;endoplasmic reticulum
• Molecular function: guanosine-diphosphatase activity;protein binding;nucleoside-diphosphatase activity;uridine-diphosphatase activity