ENTPD7

ectonucleoside triphosphate diphosphohydrolase 7, the group of Ectonucleoside triphosphate diphosphohydrolase family

Basic information

Region (hg38): 10:99659508-99711241

Links

ENSG00000198018 ∙ NCBI:57089 ∙ OMIM:616753 ∙ HGNC:19745 ∙ Uniprot:Q9NQZ7 ∙ 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 ENTPD7 gene.

• Leigh syndrome (35 variants)
• Inborn genetic diseases (22 variants)
• Cytochrome-c oxidase deficiency disease (4 variants)
• not provided (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENTPD7 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			21	1		22
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			29	4	4	37
Total	0	0	51	5	4

Variants in ENTPD7

This is a list of pathogenic ClinVar variants found in the ENTPD7 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-99661502-G-A		not specified	Uncertain significance (Jan 22, 2024)
10-99661513-C-T		not specified	Uncertain significance (Dec 31, 2023)
10-99661514-G-A		not specified	Uncertain significance (Dec 18, 2023)
10-99661567-A-G		not specified	Uncertain significance (Oct 26, 2021)
10-99661618-C-A		not specified	Uncertain significance (May 03, 2023)
10-99679263-A-C		not specified	Uncertain significance (Mar 21, 2023)
10-99679412-A-G		not specified	Uncertain significance (Apr 07, 2022)
10-99679441-A-C		not specified	Uncertain significance (May 08, 2023)
10-99679458-T-C		not specified	Uncertain significance (Jan 26, 2022)
10-99679802-G-T		not specified	Uncertain significance (Feb 28, 2024)
10-99679862-C-T		not specified	Uncertain significance (May 23, 2023)
10-99685842-T-C		not specified	Uncertain significance (Dec 09, 2023)
10-99691424-G-A		not specified	Uncertain significance (Aug 10, 2021)
10-99696022-G-A		not specified	Uncertain significance (Feb 07, 2023)
10-99696074-G-A		not specified	Uncertain significance (Dec 22, 2023)
10-99696080-G-A		not specified	Uncertain significance (Aug 30, 2021)
10-99696121-A-G		not specified	Uncertain significance (Jun 01, 2023)
10-99698707-C-T		not specified	Uncertain significance (Aug 08, 2023)
10-99698732-A-G		not specified	Uncertain significance (Dec 15, 2022)
10-99698734-A-T		not specified	Uncertain significance (Jul 12, 2023)
10-99698831-TG-T		not specified	Uncertain significance (Jul 30, 2015)
10-99702539-G-A		not specified	Uncertain significance (Dec 27, 2023)
10-99702592-G-A		not specified	Likely benign (Mar 07, 2023)
10-99702598-C-A		not specified	Uncertain significance (Feb 28, 2023)
10-99702606-G-A		not specified	Uncertain significance (May 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENTPD7	protein_coding	protein_coding	ENST00000370489	12	46735

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.13e-11	0.960	125466	2	280	125748	0.00112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.878	294	340	0.866	0.0000188	3899
Missense in Polyphen		81	106.75	0.75879		1239
Synonymous	-0.593	135	127	1.07	0.00000662	1223
Loss of Function	2.18	23	37.4	0.616	0.00000246	361

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000663	0.000662
Ashkenazi Jewish	0.00237	0.00228
East Asian	0.000437	0.000435
Finnish	0.00295	0.00282
European (Non-Finnish)	0.00122	0.00120
Middle Eastern	0.000437	0.000435
South Asian	0.00105	0.00105
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Preferentially hydrolyzes nucleoside 5'-triphosphates. The order of activity with respect to possible substrates is UTP > GTP > CTP.
• Pathway: Nucleobase catabolism;Metabolism of nucleotides;Phosphate bond hydrolysis by NTPDase proteins;Metabolism (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.882
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62

Haploinsufficiency Scores

• pHI: 0.307
• hipred: N
• hipred_score: 0.443
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.161

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Entpd7
• Phenotype: digestive/alimentary phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: nucleobase-containing small molecule catabolic process
• Cellular component: integral component of membrane;endocytic vesicle membrane
• Molecular function: nucleoside-triphosphatase activity;metal ion binding