ENTPD4

ectonucleoside triphosphate diphosphohydrolase 4, the group of Ectonucleoside triphosphate diphosphohydrolase family

Basic information

Region (hg38): 8:23385783-23457695

Previous symbols: [ "LYSAL1" ]

Links

ENSG00000197217 ∙ NCBI:9583 ∙ OMIM:607577 ∙ HGNC:14573 ∙ Uniprot:Q9Y227 ∙ 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 ENTPD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENTPD4 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			61	5		66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	61	6	0

Variants in ENTPD4

This is a list of pathogenic ClinVar variants found in the ENTPD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-23432939-G-A		not specified	Uncertain significance (Feb 28, 2024)
8-23432952-C-T		not specified	Likely benign (Sep 01, 2021)
8-23433017-C-T		not specified	Uncertain significance (Dec 15, 2023)
8-23433060-C-A		not specified	Uncertain significance (Aug 10, 2021)
8-23433067-G-C		not specified	Uncertain significance (Nov 09, 2021)
8-23433083-T-C		not specified	Uncertain significance (Apr 17, 2024)
8-23433099-A-T		not specified	Uncertain significance (Aug 04, 2021)
8-23433122-T-A		not specified	Uncertain significance (Apr 09, 2024)
8-23433131-C-T		not specified	Uncertain significance (Dec 04, 2024)
8-23433137-G-A		not specified	Uncertain significance (Feb 15, 2023)
8-23434323-G-A		not specified	Uncertain significance (Jan 08, 2025)
8-23434333-G-A		not specified	Uncertain significance (Jul 06, 2021)
8-23434388-C-A		not specified	Uncertain significance (Mar 07, 2023)
8-23435396-G-C		not specified	Uncertain significance (May 01, 2022)
8-23435399-T-C		not specified	Uncertain significance (May 09, 2024)
8-23435413-T-A		not specified	Uncertain significance (Oct 10, 2023)
8-23435413-T-C		not specified	Uncertain significance (May 20, 2024)
8-23435420-C-T		not specified	Uncertain significance (Jan 19, 2025)
8-23435431-C-T		not specified	Uncertain significance (Sep 20, 2023)
8-23435440-C-A		not specified	Uncertain significance (Jun 13, 2023)
8-23435447-G-A		not specified	Uncertain significance (Feb 20, 2025)
8-23435460-C-G		not specified	Uncertain significance (Jun 13, 2023)
8-23435467-G-T		not specified	Uncertain significance (Aug 27, 2024)
8-23436976-C-G		not specified	Uncertain significance (Dec 02, 2022)
8-23437004-T-C		not specified	Uncertain significance (Nov 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENTPD4	protein_coding	protein_coding	ENST00000358689	12	71913

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.81e-16	0.313	125549	0	199	125748	0.000792

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.723	403	364	1.11	0.0000212	4029
Missense in Polyphen		180	169.26	1.0635		1880
Synonymous	-0.658	152	142	1.07	0.00000874	1215
Loss of Function	1.47	30	40.0	0.750	0.00000287	351

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00113
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000435	0.000435
Finnish	0.000557	0.000554
European (Non-Finnish)	0.00103	0.00102
Middle Eastern	0.000435	0.000435
South Asian	0.000944	0.000915
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes preferentially nucleoside 5'-diphosphates, nucleoside 5'-triphosphates are hydrolyzed only to a minor extent. The order of activity with different substrates is UDP >> GDP = CDP = TDP, AMP, ADP, ATP and UMP are not substrates. Preferred substrates for isoform 2 are CTP, UDP, CDP, GTP and GDP, while isoform 1 utilizes UTP and TTP.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Lysosome - Homo sapiens (human);Purine metabolism - Homo sapiens (human);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: 0.157

Intolerance Scores

• loftool: 0.948
• rvis_EVS: -0.66
• rvis_percentile_EVS: 15.95

Haploinsufficiency Scores

• pHI: 0.479
• hipred: N
• hipred_score: 0.365
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.779

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Entpd4b

Gene ontology

• Biological process: UDP catabolic process;nucleobase-containing small molecule catabolic process
• Cellular component: Golgi membrane;integral component of Golgi membrane;cytoplasmic vesicle;integral component of autophagosome membrane
• Molecular function: nucleoside-diphosphatase activity;nucleoside-triphosphatase activity;uridine-diphosphatase activity