ENTPD6

ectonucleoside triphosphate diphosphohydrolase 6, the group of Ectonucleoside triphosphate diphosphohydrolase family

Basic information

Region (hg38): 20:25195693-25228075

Previous symbols: [ "CD39L2", "IL6ST2" ]

Links

ENSG00000197586 ∙ ∙ OMIM:603160 ∙ HGNC:3368 ∙ Uniprot:O75354 ∙ 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 ENTPD6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENTPD6 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			23	3		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	3	1

Variants in ENTPD6

This is a list of pathogenic ClinVar variants found in the ENTPD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-25206583-T-C		not specified	Uncertain significance (Dec 19, 2022)
20-25207087-C-A		not specified	Uncertain significance (Dec 27, 2023)
20-25207179-T-C		not specified	Uncertain significance (May 24, 2023)
20-25207184-A-G		not specified	Uncertain significance (Jul 20, 2021)
20-25207220-G-A		not specified	Uncertain significance (Apr 28, 2022)
20-25207251-C-G		not specified	Uncertain significance (Mar 25, 2024)
20-25207262-G-C		not specified	Uncertain significance (Oct 17, 2023)
20-25207328-G-A		not specified	Uncertain significance (Jun 29, 2023)
20-25207368-A-C		not specified	Uncertain significance (May 23, 2023)
20-25209858-C-T		not specified	Uncertain significance (Mar 29, 2022)
20-25213366-G-A		not specified	Uncertain significance (Sep 16, 2021)
20-25214913-G-A		not specified	Uncertain significance (Mar 20, 2023)
20-25216654-T-G		not specified	Uncertain significance (Dec 17, 2023)
20-25216716-G-A		not specified	Likely benign (Dec 07, 2023)
20-25216721-C-G		not specified	Uncertain significance (Dec 20, 2023)
20-25216728-C-T		not specified	Uncertain significance (Jun 18, 2021)
20-25216729-G-A		not specified	Uncertain significance (Dec 12, 2022)
20-25217545-G-A		not specified	Likely benign (Apr 12, 2022)
20-25218563-G-A		not specified	Uncertain significance (Nov 13, 2023)
20-25221235-A-T		not specified	Uncertain significance (Apr 13, 2022)
20-25222852-G-A		not specified	Uncertain significance (Feb 06, 2024)
20-25222894-G-A		not specified	Uncertain significance (Apr 19, 2024)
20-25222904-C-T		not specified	Uncertain significance (Nov 08, 2022)
20-25222951-G-A		not specified	Uncertain significance (Sep 16, 2021)
20-25222961-C-T		not specified	Uncertain significance (Jun 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENTPD6	protein_coding	protein_coding	ENST00000376652	14	31037

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000118	0.988	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.766	261	298	0.875	0.0000185	3110
Missense in Polyphen		85	109.86	0.77373		1202
Synonymous	0.747	118	129	0.916	0.00000901	976
Loss of Function	2.29	14	26.8	0.522	0.00000121	318

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000549	0.000541
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000220	0.000217
South Asian	0.000359	0.000327
Other	0.000335	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Might support glycosylation reactions in the Golgi apparatus and, when released from cells, might catalyze the hydrolysis of extracellular nucleotides. Hydrolyzes preferentially nucleoside 5'-diphosphates, nucleoside 5'-triphosphates are hydrolyzed only to a minor extent, there is no hydrolysis of nucleoside 5'-monophosphates. The order of activity with different substrates is GDP > IDP >> UDP = CDP >> ADP (By similarity). {ECO:0000250}.
• Pathway: Pyrimidine metabolism - 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: 0.119

Intolerance Scores

• loftool: 0.848
• rvis_EVS: 0.94
• rvis_percentile_EVS: 89.86

Haploinsufficiency Scores

• pHI: 0.176
• hipred: N
• hipred_score: 0.250
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.608

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Entpd6
• Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; skeleton phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: response to magnesium ion;nucleobase-containing small molecule catabolic process;response to calcium ion
• Cellular component: Golgi membrane;extracellular region;extracellular space;Golgi apparatus;plasma membrane;cell surface;integral component of membrane
• Molecular function: guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity;nucleoside-diphosphatase activity;nucleoside-triphosphatase activity;uridine-diphosphatase activity