1-88786179-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_006256.4(PKN2):c.1247C>T(p.Ser416Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006256.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PKN2 | ENST00000370521.8 | c.1247C>T | p.Ser416Leu | missense_variant | Exon 8 of 22 | 1 | NM_006256.4 | ENSP00000359552.3 | ||
PKN2 | ENST00000370513.9 | c.1247C>T | p.Ser416Leu | missense_variant | Exon 8 of 21 | 1 | ENSP00000359544.5 | |||
PKN2 | ENST00000316005.11 | c.1247C>T | p.Ser416Leu | missense_variant | Exon 8 of 11 | 5 | ENSP00000317851.7 | |||
PKN2 | ENST00000436111.1 | c.404C>T | p.Ser135Leu | missense_variant | Exon 3 of 5 | 3 | ENSP00000401125.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249330Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135272
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1457540Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 725322
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1247C>T (p.S416L) alteration is located in exon 8 (coding exon 8) of the PKN2 gene. This alteration results from a C to T substitution at nucleotide position 1247, causing the serine (S) at amino acid position 416 to be replaced by a leucine (L). 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