rs28702860
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002710.4(PPP1CC):c.589G>A(p.Asp197Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Consequence
PPP1CC
NM_002710.4 missense
NM_002710.4 missense
Scores
7
6
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.81
Genes affected
PPP1CC (HGNC:9283): (protein phosphatase 1 catalytic subunit gamma) The protein encoded by this gene belongs to the protein phosphatase family, PP1 subfamily. PP1 is an ubiquitous serine/threonine phosphatase that regulates many cellular processes, including cell division. It is expressed in mammalian cells as three closely related isoforms, alpha, beta/delta and gamma, which have distinct localization patterns. This gene encodes the gamma isozyme. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP1CC | NM_002710.4 | c.589G>A | p.Asp197Asn | missense_variant | 5/7 | ENST00000335007.10 | NP_002701.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP1CC | ENST00000335007.10 | c.589G>A | p.Asp197Asn | missense_variant | 5/7 | 1 | NM_002710.4 | ENSP00000335084.5 | ||
PPP1CC | ENST00000550261.5 | n.*8G>A | non_coding_transcript_exon_variant | 2/5 | 5 | ENSP00000447528.2 | ||||
PPP1CC | ENST00000550261.5 | n.*8G>A | 3_prime_UTR_variant | 2/5 | 5 | ENSP00000447528.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Pathogenic
D;.;T;D;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.;.;.;.
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D;.;D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;.;D;D;D
Sift4G
Benign
T;T;D;T;T;T
Polyphen
P;.;.;.;.;.
Vest4
MutPred
Gain of catalytic residue at V195 (P = 0.0067);Gain of catalytic residue at V195 (P = 0.0067);.;.;Gain of catalytic residue at V195 (P = 0.0067);Gain of catalytic residue at V195 (P = 0.0067);
MVP
MPC
1.8
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at