ENTPD3

protein-coding

ectonucleoside triphosphate diphosphohydrolase 3, the group of Ectonucleoside triphosphate diphosphohydrolase family

Gene summary

This gene encodes a plasma membrane-bound divalent cation-dependent E-type nucleotidase. The encoded protein is involved in the regulation of extracellular levels of ATP by hydrolysis of it and other nucleotides. Multiple transcript variants have been described. [provided by RefSeq, May 2014]

Previous symbols:

CD39L3

MANE transcript

NM_001248.4

Inheritance

—

ClinVar variants

U:71B:4

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 1.17

Max pathogenic AF

—

Genomic locus

chr3:40,387,184-40,428,744

External References & Databases

Ensembl (ENSG00000168032)

Transcript & Mutation Effects

hg38 • Region Span ~41.6 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 ENTPD3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 2

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001248.4. 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	2 clinvar		3
missense			69 clinvar	2 clinvar		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	71	4	0	75

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001248.4	RefSeq	NP_001239.2	10	MANE Select
ENST00000301825.8	Ensembl	ENSP00000301825.3	10	MANE Select
NM_001291960.2	RefSeq	NP_001278889.1	10	Standard
NM_001291961.2	RefSeq	NP_001278890.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Pyrimidine metabolism - Homo sapiens (human)
Purine metabolism - Homo sapiens (human)
Epstein-Barr virus infection - Homo sapiens (human)
Pyrimidine metabolism
Nucleobase catabolism

Biological Process

nucleoside diphosphate catabolic process
nucleoside triphosphate catabolic process
nucleobase-containing small molecule catabolic process

Molecular Function

protein binding
ATP binding
nucleoside-diphosphatase activity
nucleoside-triphosphatase activity
dATP phosphohydrolase activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000301825
Coding exons: 10
Length: 41464
Individuals with no LoFs: 125570
Homozygous LoFs: 0
Heterozygous LoFs: 177
Defined: 125747
p: 0.000704

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0684	285	288	0.989	0.0000145	3479
Missense (PolyPhen)		125	109.39	1.1427		1330
Synonymous	0.949	98	111	0.885	0.00000585	1020
Loss of Function	-0.796	29	24.7	1.17	0.00000113	292

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0014	notable
Latino/Admixed American	0.00094	0.00093	rare
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.0015	0.0015	notable
Finnish	0.00088	0.00088	rare
European (Non-Finnish)	0.00047	0.00047	rare
South Asian	0.00059	0.00056	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Has a threefold preference for the hydrolysis of ATP over ADP.;

Recessive Scores

pRec: 0.169

Intolerance Scores

LoFtool: 0.964
RVIS EVS: -0.27
RVIS percentile EVS: 34.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0775

Gene Damage Prediction

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