1-201293945-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001005337.3(PKP1):c.206C>A(p.Ser69Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000000687 in 1,456,394 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. S69T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001005337.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKP1 | NM_001005337.3 | c.206C>A | p.Ser69Tyr | missense_variant | 2/14 | ENST00000367324.8 | |
PKP1 | NM_000299.4 | c.206C>A | p.Ser69Tyr | missense_variant | 2/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKP1 | ENST00000367324.8 | c.206C>A | p.Ser69Tyr | missense_variant | 2/14 | 1 | NM_001005337.3 | P1 | |
PKP1 | ENST00000263946.7 | c.206C>A | p.Ser69Tyr | missense_variant | 2/15 | 5 | |||
PKP1 | ENST00000352845.3 | c.206C>A | p.Ser69Tyr | missense_variant | 2/14 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1456394Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 724678
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 21, 2023 | The c.206C>A (p.S69Y) alteration is located in exon 2 (coding exon 2) of the PKP1 gene. This alteration results from a C to A substitution at nucleotide position 206, causing the serine (S) at amino acid position 69 to be replaced by a tyrosine (Y). 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
Publications
No publications associated with this variant yet.