9-128705465-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_013355.5(PKN3):c.187C>T(p.Arg63Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000158 in 1,571,170 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R63H) has been classified as Uncertain significance.
Frequency
Consequence
NM_013355.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKN3 | NM_013355.5 | c.187C>T | p.Arg63Cys | missense_variant | 2/22 | ENST00000291906.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKN3 | ENST00000291906.5 | c.187C>T | p.Arg63Cys | missense_variant | 2/22 | 1 | NM_013355.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000928 AC: 16AN: 172494Hom.: 0 AF XY: 0.000117 AC XY: 11AN XY: 93998
GnomAD4 exome AF: 0.000163 AC: 231AN: 1418832Hom.: 0 Cov.: 32 AF XY: 0.000141 AC XY: 99AN XY: 702124
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152338Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.187C>T (p.R63C) alteration is located in exon 2 (coding exon 2) of the PKN3 gene. This alteration results from a C to T substitution at nucleotide position 187, causing the arginine (R) at amino acid position 63 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at