ENPP7

ectonucleotide pyrophosphatase/phosphodiesterase 7, the group of Ectonucleotide pyrophosphatase/phosphodiesterase family

Basic information

Region (hg38): 17:79730943-79742219

Links

ENSG00000182156 ∙ NCBI:339221 ∙ OMIM:616997 ∙ HGNC:23764 ∙ Uniprot:Q6UWV6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 7.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_178543.5	NP_848638.3	5	yes	-
ENST00000328313.10	ENSP00000332656.5	5	yes	-
ENST00000576512.1	ENSP00000460429.1	3	-	-
ENST00000864480.1	ENSP00000534539.1	5	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ENPP7 gene.

• not_specified (101 variants)
• not_provided (1 variants)
• Prostate_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENPP7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_178543.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			88	13		101
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	89	15	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENPP7	protein_coding	protein_coding	ENST00000328313	5	11341

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		121845	237	3666	125748	0.0156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.478	326	303	1.08	0.0000212	2989
Missense in Polyphen		130	119.33	1.0894		1320
Synonymous	0.333	136	141	0.964	0.0000117	941
Loss of Function	-0.961	19	15.0	1.27	7.32e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.121	0.120
Ashkenazi Jewish	0.00319	0.00308
East Asian	0.0000545	0.0000544
Finnish	0.000464	0.000462
European (Non-Finnish)	0.000439	0.000431
Middle Eastern	0.0000545	0.0000544
South Asian	0.000231	0.000229
Other	0.0115	0.0111

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Converts sphingomyelin to ceramide and phosphocholine (PubMed:12885774, PubMed:12671034, PubMed:15205117, PubMed:28292932). Has also phospholipase C activity and can cleave phosphocholine from palmitoyl lyso-phosphatidylcholine (PubMed:12885774). Does not have nucleotide pyrophosphatase activity (PubMed:12885774). {ECO:0000269|PubMed:12671034, ECO:0000269|PubMed:12885774, ECO:0000269|PubMed:15205117, ECO:0000269|PubMed:28292932}.
• Pathway: Sphingolipid metabolism - Homo sapiens (human);Sphingolipid Metabolism;Gaucher Disease;Globoid Cell Leukodystrophy;Metachromatic Leukodystrophy (MLD);Fabry disease;Krabbe disease;Metabolism of lipids;sphingomyelin metabolism/ceramide salvage;Metabolism;Glycosphingolipid metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.715
• rvis_EVS: 0.52
• rvis_percentile_EVS: 80.36

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.979

Gene Damage Prediction

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

Gene ontology

• Biological process: sphingomyelin metabolic process;sphingomyelin catabolic process;glycosphingolipid metabolic process;negative regulation of DNA replication;negative regulation of cell population proliferation
• Cellular component: Golgi apparatus;plasma membrane;integral component of plasma membrane;microvillus;membrane
• Molecular function: sphingomyelin phosphodiesterase activity;zinc ion binding