ENPP5

ectonucleotide pyrophosphatase/phosphodiesterase family member 5, the group of Ectonucleotide pyrophosphatase/phosphodiesterase family

Basic information

Region (hg38): 6:46159184-46170980

Links

ENSG00000112796 ∙ NCBI:59084 ∙ OMIM:617001 ∙ HGNC:13717 ∙ Uniprot:Q9UJA9 ∙ 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 ENPP5 gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENPP5 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in ENPP5

This is a list of pathogenic ClinVar variants found in the ENPP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-46161424-C-A		not specified	Uncertain significance (Jan 03, 2022)
6-46161615-T-C		not specified	Uncertain significance (Nov 27, 2023)
6-46161691-G-A		not specified	Uncertain significance (Nov 03, 2022)
6-46161709-T-C		not specified	Uncertain significance (Sep 14, 2022)
6-46165437-A-G		not specified	Uncertain significance (Dec 03, 2021)
6-46165467-T-C		not specified	Uncertain significance (Nov 04, 2021)
6-46165492-C-G		not specified	Uncertain significance (Apr 04, 2023)
6-46165549-C-T		not specified	Uncertain significance (Jan 04, 2024)
6-46167466-T-A		not specified	Uncertain significance (Jul 05, 2022)
6-46167472-A-G		not specified	Uncertain significance (Dec 14, 2021)
6-46167632-T-C		not specified	Uncertain significance (Jan 02, 2024)
6-46167651-C-T		not specified	Uncertain significance (Nov 29, 2023)
6-46167670-C-T		not specified	Uncertain significance (Dec 14, 2023)
6-46167739-G-A		not specified	Uncertain significance (Oct 25, 2022)
6-46167764-C-T		not specified	Uncertain significance (Jun 06, 2023)
6-46167818-G-A		not specified	Likely benign (Mar 11, 2024)
6-46167863-T-A		not specified	Uncertain significance (Dec 19, 2022)
6-46167980-T-C		not specified	Uncertain significance (Jan 03, 2024)
6-46168101-A-C		not specified	Uncertain significance (Sep 14, 2021)
6-46168120-G-A		not specified	Uncertain significance (Mar 01, 2024)
6-46168121-T-C		not specified	Uncertain significance (Feb 14, 2023)
6-46168219-A-G		not specified	Uncertain significance (Aug 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENPP5	protein_coding	protein_coding	ENST00000371383	3	11785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.16e-10	0.0894	125671	0	76	125747	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0436	254	256	0.992	0.0000127	3173
Missense in Polyphen		100	100.64	0.99363		1250
Synonymous	0.669	86	94.3	0.912	0.00000526	890
Loss of Function	0.153	15	15.7	0.958	7.32e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000360	0.000360
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000352	0.000334
Middle Eastern	0.000163	0.000163
South Asian	0.000699	0.000686
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can hydrolyze NAD but cannot hydrolyze nucleotide di- and triphosphates. Lacks lysopholipase D activity. May play a role in neuronal cell communication. {ECO:0000250|UniProtKB:P84039, ECO:0000250|UniProtKB:Q9EQG7}.

Recessive Scores

• pRec: 0.0878

Intolerance Scores

• loftool: 0.728
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.07

Haploinsufficiency Scores

• pHI: 0.0952
• hipred: N
• hipred_score: 0.289
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.202

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Enpp5

Gene ontology

• Biological process: cell communication
• Cellular component: extracellular region;plasma membrane;integral component of membrane
• Molecular function: hydrolase activity;metal ion binding