ENPP7

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

Basic information

Region (hg38): 17:79730943-79742219

Links

ENSG00000182156NCBI:339221OMIM:616997HGNC:23764Uniprot:Q6UWV6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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
28
clinvar
6
clinvar
34
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 28 6 0

Variants in ENPP7

This is a list of pathogenic ClinVar variants found in the ENPP7 region.

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

Position Type Phenotype Significance ClinVar
17-79731180-C-T not specified Uncertain significance (Jan 30, 2024)3089039
17-79731207-C-T Malignant tumor of prostate Uncertain significance (-)161838
17-79731275-G-C not specified Uncertain significance (Jan 11, 2023)2470682
17-79731284-G-A not specified Uncertain significance (Jan 26, 2022)3089035
17-79731333-G-A not specified Uncertain significance (Nov 09, 2021)3089036
17-79733566-G-T not specified Uncertain significance (Apr 01, 2024)2345376
17-79733618-G-A not specified Uncertain significance (Mar 28, 2024)3275507
17-79733624-G-A not specified Uncertain significance (Jul 20, 2021)3089038
17-79735107-C-T not specified Uncertain significance (Jan 09, 2024)3089040
17-79735164-C-T not specified Uncertain significance (Jun 02, 2024)3275509
17-79735277-A-G not specified Uncertain significance (Apr 12, 2024)3275506
17-79735292-C-T not specified Uncertain significance (Dec 27, 2023)3089041
17-79735298-G-A not specified Uncertain significance (Mar 21, 2024)3275511
17-79735304-C-T not specified Uncertain significance (Apr 15, 2024)3089042
17-79735320-T-A not specified Uncertain significance (Jul 14, 2021)2210496
17-79735334-G-A not specified Uncertain significance (Feb 07, 2023)2459336
17-79735352-G-A not specified Uncertain significance (Oct 12, 2021)2254420
17-79735361-A-G not specified Uncertain significance (Feb 13, 2024)3089043
17-79735385-G-A not specified Uncertain significance (Jun 07, 2024)3275516
17-79735392-C-T not specified Uncertain significance (Sep 16, 2021)2381535
17-79735407-G-A not specified Likely benign (Jun 13, 2023)2549972
17-79735415-G-A not specified Uncertain significance (Feb 06, 2024)3089045
17-79735454-C-T not specified Uncertain significance (Dec 13, 2023)3089046
17-79735488-C-T not specified Uncertain significance (Oct 06, 2021)3089047
17-79735574-A-C not specified Uncertain significance (Apr 09, 2024)3275513

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ENPP7protein_codingprotein_codingENST00000328313 511341
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.18e-140.0031412184523736661257480.0156
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4783263031.080.00002122989
Missense in Polyphen130119.331.08941320
Synonymous0.3331361410.9640.0000117941
Loss of Function-0.9611915.01.277.32e-7161

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.1210.120
Ashkenazi Jewish0.003190.00308
East Asian0.00005450.0000544
Finnish0.0004640.000462
European (Non-Finnish)0.0004390.000431
Middle Eastern0.00005450.0000544
South Asian0.0002310.000229
Other0.01150.0111

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

Haploinsufficiency Scores

pHI
0.0944
hipred
N
hipred_score
0.275
ghis
0.416

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Enpp7
Phenotype
digestive/alimentary phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype;

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