ENTPD3

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

Basic information

Region (hg38): 3:40387184-40428744

Previous symbols: [ "CD39L3" ]

Links

ENSG00000168032 ∙ NCBI:956 ∙ OMIM:603161 ∙ HGNC:3365 ∙ Uniprot:O75355 ∙ 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 ENTPD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENTPD3 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			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	0

Variants in ENTPD3

This is a list of pathogenic ClinVar variants found in the ENTPD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-40392031-G-T		not specified	Uncertain significance (Mar 29, 2023)
3-40392062-T-G		not specified	Uncertain significance (Dec 16, 2021)
3-40392091-C-T		not specified	Uncertain significance (May 08, 2024)
3-40392109-A-T		not specified	Uncertain significance (Jun 07, 2023)
3-40400927-A-G		not specified	Uncertain significance (May 04, 2022)
3-40400928-C-T		not specified	Uncertain significance (May 20, 2024)
3-40411827-G-C		not specified	Uncertain significance (Jan 23, 2023)
3-40411872-G-A		not specified	Uncertain significance (Dec 08, 2023)
3-40411913-G-A		not specified	Uncertain significance (Jul 02, 2024)
3-40411941-C-T		not specified	Uncertain significance (Aug 17, 2022)
3-40411942-G-A			Likely benign (Mar 01, 2023)
3-40411944-C-T		not specified	Uncertain significance (Oct 25, 2023)
3-40414706-G-A		not specified	Uncertain significance (Oct 03, 2022)
3-40414816-C-A		not specified	Uncertain significance (Feb 22, 2023)
3-40414816-C-G		not specified	Uncertain significance (Feb 15, 2023)
3-40414825-G-A		not specified	Uncertain significance (Jan 03, 2024)
3-40415858-T-G		not specified	Uncertain significance (Sep 08, 2024)
3-40415903-G-C		not specified	Uncertain significance (Mar 28, 2024)
3-40415910-C-T		not specified	Uncertain significance (May 31, 2023)
3-40416000-C-T		not specified	Uncertain significance (Dec 16, 2023)
3-40416033-G-A			Likely benign (Mar 01, 2023)
3-40416054-T-A		Malignant tumor of prostate	Uncertain significance (-)
3-40422892-C-T		not specified	Uncertain significance (Nov 20, 2024)
3-40422893-G-A		not specified	Uncertain significance (Aug 28, 2024)
3-40422947-T-G		not specified	Uncertain significance (Jun 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENTPD3	protein_coding	protein_coding	ENST00000301825	10	41464

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.64e-21	0.000267	125570	0	177	125747	0.000704

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0684	285	288	0.989	0.0000145	3479
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00230	0.00230
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.00147	0.00147
Finnish	0.000878	0.000878
European (Non-Finnish)	0.000467	0.000466
Middle Eastern	0.00147	0.00147
South Asian	0.000589	0.000555
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has a threefold preference for the hydrolysis of ATP over ADP.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Pyrimidine metabolism;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: 0.169

Intolerance Scores

• loftool: 0.964
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.82

Haploinsufficiency Scores

• pHI: 0.169
• hipred: N
• hipred_score: 0.334
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0775

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Entpd3
• 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); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: nucleoside diphosphate catabolic process;nucleoside triphosphate catabolic process;nucleobase-containing small molecule catabolic process
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding;ATP binding;nucleoside-diphosphatase activity;nucleoside-triphosphatase activity;dATP phosphohydrolase activity;dCTP phosphohydrolase activity;dUTP phosphohydrolase activity;dTTP phosphohydrolase activity;GTP phosphohydrolase activity;8-oxo-dGTP phosphohydrolase activity;dGTP phosphohydrolase activity