6-127973096-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP2PP3BS2
The NM_002844.4(PTPRK):c.4195C>T(p.Arg1399Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,613,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R1399Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_002844.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRK | NM_002844.4 | c.4195C>T | p.Arg1399Trp | missense_variant | 29/30 | ENST00000368226.9 | |
PTPRK | NM_001291981.2 | c.4261C>T | p.Arg1421Trp | missense_variant | 32/33 | ||
PTPRK | NM_001135648.3 | c.4213C>T | p.Arg1405Trp | missense_variant | 30/31 | ||
PTPRK | NM_001291984.2 | c.4192C>T | p.Arg1398Trp | missense_variant | 29/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRK | ENST00000368226.9 | c.4195C>T | p.Arg1399Trp | missense_variant | 29/30 | 1 | NM_002844.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251168Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135722
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461796Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727216
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 05, 2023 | The c.4213C>T (p.R1405W) alteration is located in exon 30 (coding exon 30) of the PTPRK gene. This alteration results from a C to T substitution at nucleotide position 4213, causing the arginine (R) at amino acid position 1405 to be replaced by a tryptophan (W). 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