5-134197777-G-GGAA
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4_SupportingPP5_Moderate
The NM_002715.4(PPP2CA):c.924_925insTTC(p.Phe308dup) variant causes a inframe insertion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Consequence
PPP2CA
NM_002715.4 inframe_insertion
NM_002715.4 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.44
Genes affected
PPP2CA (HGNC:9299): (protein phosphatase 2 catalytic subunit alpha) This gene encodes the phosphatase 2A catalytic subunit. Protein phosphatase 2A is one of the four major Ser/Thr phosphatases, and it is implicated in the negative control of cell growth and division. It consists of a common heteromeric core enzyme, which is composed of a catalytic subunit and a constant regulatory subunit, that associates with a variety of regulatory subunits. This gene encodes an alpha isoform of the catalytic subunit. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_002715.4. Strenght limited to Supporting due to length of the change: 1aa.
PP5
Variant 5-134197777-G-GGAA is Pathogenic according to our data. Variant chr5-134197777-G-GGAA is described in ClinVar as [Likely_pathogenic]. Clinvar id is 620081.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2CA | NM_002715.4 | c.924_925insTTC | p.Phe308dup | inframe_insertion | 7/7 | ENST00000481195.6 | |
PPP2CA | NM_001355019.2 | c.729_730insTTC | p.Phe243dup | inframe_insertion | 7/7 | ||
PPP2CA | NR_149151.2 | n.1179_1180insTTC | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2CA | ENST00000481195.6 | c.924_925insTTC | p.Phe308dup | inframe_insertion | 7/7 | 1 | NM_002715.4 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Houge-Janssens syndrome 3 Pathogenic:2
Likely pathogenic, criteria provided, single submitter | curation | SIB Swiss Institute of Bioinformatics | Jul 15, 2019 | This variant is interpreted as a Likely pathogenic for Neurodevelopmental disorder and language delay with or without structural brain abnormalities, autosomal dominant. The following ACMG Tag(s) were applied: PM2, PM6, PS3. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 10, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at