ENTPD2

ectonucleoside triphosphate diphosphohydrolase 2, the group of Ectonucleoside triphosphate diphosphohydrolase family

Basic information

Region (hg38): 9:137048107-137054061

Previous symbols: [ "CD39L1" ]

Links

ENSG00000054179 ∙ NCBI:954 ∙ OMIM:602012 ∙ HGNC:3364 ∙ Uniprot:Q9Y5L3 ∙ 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 ENTPD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENTPD2 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	2
missense			59	3	2	64
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	1	59	4	3

Variants in ENTPD2

This is a list of pathogenic ClinVar variants found in the ENTPD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-137048700-A-C		not specified	Uncertain significance (Feb 07, 2025)
9-137048701-G-C		not specified	Uncertain significance (Feb 07, 2025)
9-137048707-C-T			Benign (Dec 31, 2019)
9-137048716-C-T		not specified	Uncertain significance (Oct 29, 2021)
9-137048779-G-A		not specified	Uncertain significance (Sep 01, 2021)
9-137048787-G-A		not specified	Uncertain significance (Aug 15, 2023)
9-137048803-T-C		not specified	Uncertain significance (Nov 11, 2024)
9-137048820-A-G		not specified	Uncertain significance (Mar 29, 2024)
9-137048824-T-G		not specified	Uncertain significance (Mar 14, 2023)
9-137048835-G-A		not specified	Uncertain significance (Feb 05, 2024)
9-137048856-G-C		not specified	Likely benign (Jan 16, 2024)
9-137048936-C-T			Likely benign (Nov 01, 2022)
9-137048960-C-G		not specified	Uncertain significance (Jul 13, 2021)
9-137048961-C-T		not specified	Uncertain significance (Nov 23, 2022)
9-137048964-C-G		not specified	Uncertain significance (Dec 10, 2024)
9-137048984-C-T		not specified	Uncertain significance (Mar 10, 2025)
9-137048991-C-G		not specified	Uncertain significance (Aug 21, 2023)
9-137048999-A-G		not specified	Uncertain significance (Nov 26, 2024)
9-137049024-C-T		not specified	Uncertain significance (Jul 20, 2022)
9-137049048-C-A		not specified	Uncertain significance (Jun 22, 2021)
9-137049050-C-G		not specified	Uncertain significance (Jun 22, 2021)
9-137049051-G-A		not specified	Uncertain significance (Mar 02, 2023)
9-137049054-GC-G		Susceptibility to severe COVID-19	Likely pathogenic (Jul 22, 2024)
9-137049068-G-A		not specified	Uncertain significance (Jan 23, 2024)
9-137049932-C-T		not specified	Uncertain significance (Jun 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENTPD2	protein_coding	protein_coding	ENST00000355097	9	5948

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.46e-14	0.0132	125593	1	64	125658	0.000259

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.659	299	269	1.11	0.0000154	3125
Missense in Polyphen		110	102.81	1.0699		1330
Synonymous	-0.453	123	117	1.05	0.00000694	1074
Loss of Function	-0.0940	21	20.5	1.02	0.00000114	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000367	0.000364
Ashkenazi Jewish	0.000306	0.000298
East Asian	0.000164	0.000163
Finnish	0.000280	0.000277
European (Non-Finnish)	0.000403	0.000343
Middle Eastern	0.000164	0.000163
South Asian	0.000196	0.000196
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In the nervous system, could hydrolyze ATP and other nucleotides to regulate purinergic neurotransmission. Hydrolyzes ADP only to a marginal extent. The order of activity with different substrates is ATP > GTP > CTP = ITP > UTP >> ADP = UDP.
• Pathway: Purine metabolism - Homo sapiens (human);Taste transduction - Homo sapiens (human);Nucleobase catabolism;Metabolism of nucleotides;Phosphate bond hydrolysis by NTPDase proteins;Metabolism;Purine nucleotides nucleosides metabolism (Consensus)

Recessive Scores

• pRec: 0.155

Intolerance Scores

• loftool: 0.897
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.3

Haploinsufficiency Scores

• pHI: 0.262
• hipred: N
• hipred_score: 0.238
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.365

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Entpd2
• Phenotype: taste/olfaction phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;purine ribonucleoside diphosphate catabolic process;platelet activation;nucleobase-containing small molecule catabolic process
• Cellular component: basement membrane;endoplasmic reticulum membrane;plasma membrane;integral component of membrane;extracellular exosome
• Molecular function: ATP binding;nucleoside-diphosphatase activity;nucleoside-triphosphatase activity