19-14451088-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002741.5(PKN1):c.949T>A(p.Cys317Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,539,346 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002741.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKN1 | NM_002741.5 | c.949T>A | p.Cys317Ser | missense_variant | 6/22 | ENST00000242783.11 | |
PKN1 | NM_213560.3 | c.967T>A | p.Cys323Ser | missense_variant | 6/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKN1 | ENST00000242783.11 | c.949T>A | p.Cys317Ser | missense_variant | 6/22 | 1 | NM_002741.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152056Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000271 AC: 4AN: 147520Hom.: 0 AF XY: 0.0000251 AC XY: 2AN XY: 79816
GnomAD4 exome AF: 0.000115 AC: 159AN: 1387290Hom.: 1 Cov.: 35 AF XY: 0.000104 AC XY: 71AN XY: 682992
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152056Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2023 | The c.967T>A (p.C323S) alteration is located in exon 6 (coding exon 6) of the PKN1 gene. This alteration results from a T to A substitution at nucleotide position 967, causing the cysteine (C) at amino acid position 323 to be replaced by a serine (S). 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