chr20-46686787-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM5PP3PP5
The NM_033550.4(TP53RK):c.728G>T(p.Arg243Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,846 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. R243C) has been classified as Likely pathogenic.
Frequency
Consequence
NM_033550.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TP53RK | NM_033550.4 | c.728G>T | p.Arg243Leu | missense_variant | 2/2 | ENST00000372114.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TP53RK | ENST00000372114.4 | c.728G>T | p.Arg243Leu | missense_variant | 2/2 | 1 | NM_033550.4 | P1 | |
TP53RK | ENST00000372102.3 | c.*367G>T | 3_prime_UTR_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727216
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