chr20-46689290-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_033550.4(TP53RK):c.125G>A(p.Gly42Asp) variant causes a missense change. The variant allele was found at a frequency of 0.000000718 in 1,392,360 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 11/19 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G42V) has been classified as Uncertain significance.
Frequency
Consequence
NM_033550.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TP53RK | NM_033550.4 | c.125G>A | p.Gly42Asp | missense_variant | 1/2 | ENST00000372114.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TP53RK | ENST00000372114.4 | c.125G>A | p.Gly42Asp | missense_variant | 1/2 | 1 | NM_033550.4 | P1 | |
TP53RK | ENST00000372102.3 | c.125G>A | p.Gly42Asp | missense_variant | 1/2 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 7.18e-7 AC: 1AN: 1392360Hom.: 0 Cov.: 31 AF XY: 0.00000145 AC XY: 1AN XY: 688320
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Galloway-Mowat syndrome 4 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 27, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at