rs1044498

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 2P and 13B. PM1BP4_StrongBP6BA1

The NM_006208.3(ENPP1):c.517A>C(p.Lys173Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 1,613,790 control chromosomes in the GnomAD database, including 41,008 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.33 ( 14194 hom., cov: 32)

Exomes 𝑓: 0.16 ( 26814 hom. )

Consequence

ENPP1
NM_006208.3 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1B:10O:3

Conservation

PhyloP100: 1.45

Variant links:

Genes affected

ENPP1 (HGNC:3356): (ectonucleotide pyrophosphatase/phosphodiesterase 1) This gene is a member of the ecto-nucleotide pyrophosphatase/phosphodiesterase (ENPP) family. The encoded protein is a type II transmembrane glycoprotein comprising two identical disulfide-bonded subunits. This protein has broad specificity and cleaves a variety of substrates, including phosphodiester bonds of nucleotides and nucleotide sugars and pyrophosphate bonds of nucleotides and nucleotide sugars. This protein may function to hydrolyze nucleoside 5' triphosphates to their corresponding monophosphates and may also hydrolyze diadenosine polyphosphates. Mutations in this gene have been associated with 'idiopathic' infantile arterial calcification, ossification of the posterior longitudinal ligament of the spine (OPLL), and insulin resistance. [provided by RefSeq, Jul 2008]

ENPP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

PM1

In a disulfide_bond (size 13) in uniprot entity ENPP1_HUMAN there are 4 pathogenic changes around while only 1 benign (80%) in NM_006208.3

BP4

Computational evidence support a benign effect (MetaRNN=9.3244637E-7).

BP6

Variant 6-131851228-A-C is Benign according to our data. Variant chr6-131851228-A-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 13589.We mark this variant Likely_benign, oryginal submissions are: {Likely_pathogenic=1, not_provided=1, Benign=9}. Variant chr6-131851228-A-C is described in Lovd as [Likely_pathogenic].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENPP1	NM_006208.3 link	c.517A>C	p.Lys173Gln	missense_variant	Exon 4 of 25	ENST00000647893.1	NP_006199.2	P22413

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENPP1	ENST00000647893.1 link	c.517A>C	p.Lys173Gln	missense_variant	Exon 4 of 25		NM_006208.3	ENSP00000498074.1		P22413

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

49878

AN:

152022

Hom.:

14135

Cov.:

show subpopulations

Gnomad AFR

AF:

0.775

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.0944

Gnomad SAS

AF:

0.176

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.295

GnomAD2 exomes

AF:

0.195

AC:

48946

AN:

251206

AF XY:

0.183

show subpopulations

Gnomad AFR exome

AF:

0.786

Gnomad AMR exome

AF:

0.188

Gnomad ASJ exome

AF:

0.219

Gnomad EAS exome

AF:

0.0977

Gnomad FIN exome

AF:

0.128

Gnomad NFE exome

AF:

0.146

Gnomad OTH exome

AF:

0.181

GnomAD4 exome

AF:

0.162

AC:

236113

AN:

1461650

Hom.:

26814

Cov.:

AF XY:

0.159

AC XY:

115934

AN XY:

727146

show subpopulations

Gnomad4 AFR exome

AF:

0.798

AC:

26703

AN:

33472

Gnomad4 AMR exome

AF:

0.193

AC:

8616

AN:

44718

Gnomad4 ASJ exome

AF:

0.222

AC:

5790

AN:

26130

Gnomad4 EAS exome

AF:

0.0933

AC:

3702

AN:

39698

Gnomad4 SAS exome

AF:

0.171

AC:

14748

AN:

86258

Gnomad4 FIN exome

AF:

0.128

AC:

6835

AN:

53418

Gnomad4 NFE exome

AF:

0.141

AC:

156371

AN:

1111812

Gnomad4 Remaining exome

AF:

0.199

AC:

12022

AN:

60384

Heterozygous variant carriers

10393

20787

31180

41574

51967

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

5926

11852

17778

23704

29630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.329

AC:

49999

AN:

152140

Hom.:

14194

Cov.:

AF XY:

0.322

AC XY:

23968

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.776

AC:

0.775565

AN:

0.775565

Gnomad4 AMR

AF:

0.245

AC:

0.244575

AN:

0.244575

Gnomad4 ASJ

AF:

0.232

AC:

0.232277

AN:

0.232277

Gnomad4 EAS

AF:

0.0942

AC:

0.094186

AN:

0.094186

Gnomad4 SAS

AF:

0.177

AC:

0.177433

AN:

0.177433

Gnomad4 FIN

AF:

0.122

AC:

0.121716

AN:

0.121716

Gnomad4 NFE

AF:

0.142

AC:

0.142172

AN:

0.142172

Gnomad4 OTH

AF:

0.296

AC:

0.295541

AN:

0.295541

Heterozygous variant carriers

1129

2259

3388

4518

5647

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

398

796

1194

1592

1990

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.214

Hom.:

16963

Bravo

AF:

0.356

TwinsUK

AF:

0.143

AC:

530

ALSPAC

AF:

0.141

AC:

543

ESP6500AA

AF:

0.751

AC:

3310

ESP6500EA

AF:

0.145

AC:

1245

ExAC

AF:

0.206

AC:

25043

Asia WGS

AF:

0.163

AC:

570

AN:

3478

EpiCase

AF:

0.151

EpiControl

AF:

0.150

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1Benign:10Other:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Hypophosphatemic rickets, autosomal recessive, 2

Benign:2

Jul 30, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -

Arterial calcification, generalized, of infancy, 1

Benign:2

Jul 30, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -

Hypophosphatemic rickets

Pathogenic:1

Mar 07, 2022

Laboratory of Cyto-molecular Genetics, Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi

Significance:Likely pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

Apr 24, 2015

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Type 2 diabetes mellitus

Benign:1

Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:research

rs1044498 of ENPP1 is associated with type 2 diabetes mellitus and increased insulin resistance. It is also associated with calcification of coronary artery disease, increasing the chances of macrovascular complications in diabetes. -

Type 2 diabetes mellitus;C2750078:Hypophosphatemic rickets, autosomal recessive, 2;C3809781:Hypopigmentation-punctate palmoplantar keratoderma syndrome;C4054476:Inherited obesity;C4551985:Arterial calcification, generalized, of infancy, 1

Benign:1

Apr 17, 2023

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:research

- -

Hypopigmentation-punctate palmoplantar keratoderma syndrome

Benign:1

Jul 30, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

ENPP1-related disorder

Benign:1

Apr 23, 2020

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Insulin resistance, susceptibility to

Other:1

May 23, 2025

OMIM

Significance:not provided

Review Status:no classification provided

Collection Method:literature only

- -

Diabetes mellitus type 2, susceptibility to

Other:1

Dec 01, 2006

OMIM

Significance:risk factor

Review Status:no assertion criteria provided

Collection Method:literature only

- -

Obesity

Other:1

Dec 01, 2006

OMIM

Significance:risk factor

Review Status:no assertion criteria provided

Collection Method:literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Benign

0.93

DEOGEN2

Benign

0.40

T;T

Eigen

Benign

-0.74

Eigen_PC

Benign

-0.70

FATHMM_MKL

Benign

0.051

LIST_S2

Benign

0.37

.;T

MetaRNN

Benign

9.3e-7

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.8

L;L

PrimateAI

Benign

0.24

PROVEAN

Benign

-1.6

N;.

REVEL

Benign

0.055

Sift

Benign

0.32

T;.

Sift4G

Benign

0.38

T;.

Polyphen

0.072

B;B

Vest4

0.031

MPC

0.22

ClinPred

0.016

GERP RS

3.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.086

gMVP

0.59

Mutation Taster

=99/1

polymorphism (auto)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over