6-127985772-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002844.4(PTPRK):c.3200G>A(p.Arg1067Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,748 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002844.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPRK | NM_002844.4 | c.3200G>A | p.Arg1067Gln | missense_variant | Exon 22 of 30 | ENST00000368226.9 | NP_002835.2 | |
PTPRK | NM_001291981.2 | c.3266G>A | p.Arg1089Gln | missense_variant | Exon 25 of 33 | NP_001278910.1 | ||
PTPRK | NM_001135648.3 | c.3218G>A | p.Arg1073Gln | missense_variant | Exon 23 of 31 | NP_001129120.1 | ||
PTPRK | NM_001291984.2 | c.3197G>A | p.Arg1066Gln | missense_variant | Exon 22 of 30 | NP_001278913.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251286Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135810
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461622Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727110
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3218G>A (p.R1073Q) alteration is located in exon 23 (coding exon 23) of the PTPRK gene. This alteration results from a G to A substitution at nucleotide position 3218, causing the arginine (R) at amino acid position 1073 to be replaced by a glutamine (Q). 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