rs141223649
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_002711.4(PPP1R3A):c.628C>T(p.Arg210Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000174 in 1,613,214 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00093 ( 1 hom., cov: 32)
Exomes 𝑓: 0.000096 ( 1 hom. )
Consequence
PPP1R3A
NM_002711.4 missense
NM_002711.4 missense
Scores
4
7
8
Clinical Significance
Conservation
PhyloP100: 5.42
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.023028404).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP1R3A | ENST00000284601.4 | c.628C>T | p.Arg210Cys | missense_variant | Exon 1 of 4 | 1 | NM_002711.4 | ENSP00000284601.3 | ||
PPP1R3A | ENST00000284602.1 | n.179-72C>T | intron_variant | Intron 1 of 4 | 1 | ENSP00000284602.1 | ||||
PPP1R3A | ENST00000449795.5 | c.-181-36049C>T | intron_variant | Intron 1 of 3 | 3 | ENSP00000401278.1 |
Frequencies
GnomAD3 genomes AF: 0.000928 AC: 141AN: 151900Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000323 AC: 81AN: 250710Hom.: 1 AF XY: 0.000244 AC XY: 33AN XY: 135516
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GnomAD4 exome AF: 0.0000958 AC: 140AN: 1461196Hom.: 1 Cov.: 31 AF XY: 0.0000922 AC XY: 67AN XY: 726892
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GnomAD4 genome AF: 0.000928 AC: 141AN: 152018Hom.: 1 Cov.: 32 AF XY: 0.00101 AC XY: 75AN XY: 74314
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Monogenic diabetes Uncertain:1
Apr 07, 2017
Personalized Diabetes Medicine Program, University of Maryland School of Medicine
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: research
ACMG Criteria:PP3 (6 predictors), BP4 (4 predictors) -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at