rs1799999

Positions:

chr7-113878379-C-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_002711.4(PPP1R3A):c.2713G>T(p.Asp905Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,611,778 control chromosomes in the GnomAD database, including 29,281 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.17 ( 3429 hom., cov: 32)

Exomes 𝑓: 0.14 ( 25852 hom. )

Consequence

PPP1R3A
NM_002711.4 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:2O:1

Conservation

PhyloP100: 3.23

Variant links:

Genes affected

PPP1R3A (HGNC:9291): (protein phosphatase 1 regulatory subunit 3A) The glycogen-associated form of protein phosphatase-1 (PP1) derived from skeletal muscle is a heterodimer composed of a 37-kD catalytic subunit and a 124-kD targeting and regulatory subunit. This gene encodes the regulatory subunit which binds to muscle glycogen with high affinity, thereby enhancing dephosphorylation of glycogen-bound substrates for PP1 such as glycogen synthase and glycogen phosphorylase kinase. [provided by RefSeq, Jul 2008]

PPP1R3A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.817586E-6).

BP6

Variant 7-113878379-C-A is Benign according to our data. Variant chr7-113878379-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 8706.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=1}. Variant chr7-113878379-C-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP1R3A	NM_002711.4 linkuse as main transcript	c.2713G>T	p.Asp905Tyr	missense_variant	4/4	ENST00000284601.4	NP_002702.2	Q16821-1
PPP1R3A	XM_005250473.4 linkuse as main transcript	c.2110G>T	p.Asp704Tyr	missense_variant	5/5		XP_005250530.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R3A	ENST00000284601.4 linkuse as main transcript	c.2713G>T	p.Asp905Tyr	missense_variant	4/4	1	NM_002711.4	ENSP00000284601.3		Q16821-1

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26465

AN:

151784

Hom.:

3426

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.122

Gnomad AMR

AF:

0.213

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.670

Gnomad SAS

AF:

0.398

Gnomad FIN

AF:

0.204

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.0950

Gnomad OTH

AF:

0.179

GnomAD3 exomes

AF:

0.221

AC:

55132

AN:

249384

Hom.:

9572

AF XY:

0.223

AC XY:

30090

AN XY:

134852

show subpopulations

Gnomad AFR exome

AF:

0.195

Gnomad AMR exome

AF:

0.259

Gnomad ASJ exome

AF:

0.213

Gnomad EAS exome

AF:

0.684

Gnomad SAS exome

AF:

0.387

Gnomad FIN exome

AF:

0.205

Gnomad NFE exome

AF:

0.0985

Gnomad OTH exome

AF:

0.184

GnomAD4 exome

AF:

0.142

AC:

206696

AN:

1459874

Hom.:

25852

Cov.:

AF XY:

0.149

AC XY:

107979

AN XY:

726318

show subpopulations

Gnomad4 AFR exome

AF:

0.197

Gnomad4 AMR exome

AF:

0.257

Gnomad4 ASJ exome

AF:

0.216

Gnomad4 EAS exome

AF:

0.688

Gnomad4 SAS exome

AF:

0.389

Gnomad4 FIN exome

AF:

0.194

Gnomad4 NFE exome

AF:

0.0908

Gnomad4 OTH exome

AF:

0.170

GnomAD4 genome

AF:

0.174

AC:

26493

AN:

151904

Hom.:

3429

Cov.:

AF XY:

0.188

AC XY:

13954

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.193

Gnomad4 AMR

AF:

0.214

Gnomad4 ASJ

AF:

0.207

Gnomad4 EAS

AF:

0.671

Gnomad4 SAS

AF:

0.398

Gnomad4 FIN

AF:

0.204

Gnomad4 NFE

AF:

0.0950

Gnomad4 OTH

AF:

0.180

Alfa

AF:

0.133

Hom.:

4276

Bravo

AF:

0.178

TwinsUK

AF:

0.0914

AC:

339

ALSPAC

AF:

0.0867

AC:

334

ESP6500AA

AF:

0.195

AC:

858

ESP6500EA

AF:

0.105

AC:

902

ExAC

AF:

0.219

AC:

26546

Asia WGS

AF:

0.439

AC:

1524

AN:

3478

EpiCase

AF:

0.0978

EpiControl

AF:

0.0986

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:2Other:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Type 2 diabetes mellitus

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Jan 01, 2016

This variant was classified as: Uncertain significance. The following ACMG criteria were applied in classifying this variant: BP6,PP5. This variant was detected in homozygous state. -

PPP1R3A-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

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). -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

This variant is associated with the following publications: (PMID: 7581368) -

Insulin resistance, susceptibility to

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Aug 01, 1995

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.19

Eigen

Uncertain

0.50

Eigen_PC

Uncertain

0.49

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.72

MetaRNN

Benign

0.0000088

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.8

PrimateAI

Benign

0.28

PROVEAN

Uncertain

-2.4

REVEL

Benign

0.081

Sift

Pathogenic

0.0

Sift4G

Uncertain

0.014

Polyphen

0.98

Vest4

0.15

MPC

0.31

ClinPred

0.044

GERP RS

5.6

Varity_R

0.20

gMVP

0.37

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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