ENPP4

ectonucleotide pyrophosphatase/phosphodiesterase 4, the group of Ectonucleotide pyrophosphatase/phosphodiesterase family

Basic information

Region (hg38): 6:46129989-46146688

Links

ENSG00000001561 ∙ NCBI:22875 ∙ OMIM:617000 ∙ HGNC:3359 ∙ Uniprot:Q9Y6X5 ∙ 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 ENPP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENPP4 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			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	1	0

Variants in ENPP4

This is a list of pathogenic ClinVar variants found in the ENPP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-46139614-G-A		not specified	Uncertain significance (Feb 28, 2023)
6-46139651-G-C		not specified	Uncertain significance (May 15, 2023)
6-46139717-A-G		not specified	Uncertain significance (Apr 27, 2024)
6-46139765-A-G		not specified	Uncertain significance (May 17, 2023)
6-46139860-A-T		not specified	Uncertain significance (Dec 01, 2022)
6-46139881-A-G		not specified	Uncertain significance (Oct 02, 2023)
6-46139883-A-T		not specified	Uncertain significance (Jan 19, 2024)
6-46139885-A-T		not specified	Uncertain significance (Jul 13, 2021)
6-46139896-T-A		not specified	Uncertain significance (May 13, 2024)
6-46139897-C-T		not specified	Likely benign (Jan 08, 2024)
6-46139903-A-G		not specified	Uncertain significance (Dec 26, 2023)
6-46140014-A-G		not specified	Uncertain significance (May 09, 2023)
6-46140019-A-G		not specified	Uncertain significance (Dec 05, 2022)
6-46140022-A-C		not specified	Uncertain significance (Apr 13, 2022)
6-46140032-A-T		not specified	Uncertain significance (May 14, 2024)
6-46140124-G-A		not specified	Uncertain significance (Apr 06, 2023)
6-46140151-G-A		not specified	Uncertain significance (Apr 07, 2022)
6-46140152-C-A		not specified	Uncertain significance (Apr 07, 2022)
6-46140169-G-A		not specified	Uncertain significance (Oct 05, 2021)
6-46140331-A-T		not specified	Uncertain significance (Jul 09, 2021)
6-46141052-A-G		not specified	Uncertain significance (May 11, 2022)
6-46141063-G-T		not specified	Uncertain significance (Dec 20, 2023)
6-46141108-C-T		not specified	Uncertain significance (Mar 28, 2024)
6-46141154-G-A		not specified	Uncertain significance (Mar 13, 2023)
6-46141158-T-G		not specified	Uncertain significance (Jan 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENPP4	protein_coding	protein_coding	ENST00000321037	3	16707

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.119	0.876	125571	0	22	125593	0.0000876

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.803	204	239	0.854	0.0000113	3025
Missense in Polyphen		38	65.575	0.57949		799
Synonymous	0.320	84	87.8	0.957	0.00000458	844
Loss of Function	2.45	4	13.9	0.289	6.47e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000106	0.000106
Middle Eastern	0.0000544	0.0000544
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes extracellular Ap3A into AMP and ADP, and Ap4A into AMP and ATP. Ap3A and Ap4A are diadenosine polyphosphates thought to induce proliferation of vascular smooth muscle cells. Acts as a procoagulant, mediating platelet aggregation at the site of nascent thrombus via release of ADP from Ap3A and activation of ADP receptors. {ECO:0000269|PubMed:22995898, ECO:0000269|PubMed:24338010}.
• Pathway: Purine metabolism - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.686
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.0664
• hipred: Y
• hipred_score: 0.595
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.159

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Enpp4

Gene ontology

• Biological process: blood coagulation;positive regulation of blood coagulation;neutrophil degranulation;purine ribonucleoside catabolic process
• Cellular component: plasma membrane;membrane;integral component of membrane;extracellular exosome;ficolin-1-rich granule membrane
• Molecular function: metal ion binding;bis(5'-adenosyl)-triphosphatase activity