GeneBe

2-28752142-G-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7

The NM_002709.3(PPP1CB):​c.18G>A​(p.Leu6Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PPP1CB
NM_002709.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.08
Variant links:
Genes affected
PPP1CB (HGNC:9282): (protein phosphatase 1 catalytic subunit beta) The protein encoded by this gene is one of the three catalytic subunits of protein phosphatase 1 (PP1). PP1 is a serine/threonine specific protein phosphatase known to be involved in the regulation of a variety of cellular processes, such as cell division, glycogen metabolism, muscle contractility, protein synthesis, and HIV-1 viral transcription. Mouse studies suggest that PP1 functions as a suppressor of learning and memory. Two alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
Variant 2-28752142-G-A is Benign according to our data. Variant chr2-28752142-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3623123.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=3.08 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PPP1CBNM_002709.3 linkc.18G>A p.Leu6Leu synonymous_variant Exon 1 of 8 ENST00000395366.3 NP_002700.1 P62140V9HW04
PPP1CBNM_206876.2 linkc.18G>A p.Leu6Leu synonymous_variant Exon 2 of 9 NP_996759.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PPP1CBENST00000395366.3 linkc.18G>A p.Leu6Leu synonymous_variant Exon 1 of 8 1 NM_002709.3 ENSP00000378769.2 P62140

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1397254
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
689182
African (AFR)
AF:
0.00
AC:
0
AN:
31258
American (AMR)
AF:
0.00
AC:
0
AN:
35640
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25124
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35434
South Asian (SAS)
AF:
0.00
AC:
0
AN:
79218
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
48972
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5684
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1077998
Other (OTH)
AF:
0.00
AC:
0
AN:
57926
GnomAD4 genome
Cov.:
30

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Dec 25, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.41
CADD
Benign
14
DANN
Benign
0.96
PhyloP100
3.1
PromoterAI
-0.025
Neutral
Mutation Taster
=99/1
polymorphism

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

Other links and lift over

hg19: chr2-28975008; API