chr1-201293944-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001005337.3(PKP1):c.205T>A(p.Ser69Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000687 in 1,456,366 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. 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. S69Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_001005337.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKP1 | NM_001005337.3 | c.205T>A | p.Ser69Thr | missense_variant, splice_region_variant | 2/14 | ENST00000367324.8 | |
PKP1 | NM_000299.4 | c.205T>A | p.Ser69Thr | missense_variant, splice_region_variant | 2/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKP1 | ENST00000367324.8 | c.205T>A | p.Ser69Thr | missense_variant, splice_region_variant | 2/14 | 1 | NM_001005337.3 | P1 | |
PKP1 | ENST00000263946.7 | c.205T>A | p.Ser69Thr | missense_variant, splice_region_variant | 2/15 | 5 | |||
PKP1 | ENST00000352845.3 | c.205T>A | p.Ser69Thr | missense_variant, splice_region_variant | 2/14 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1456366Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 724684
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.205T>A (p.S69T) alteration is located in exon 2 (coding exon 2) of the PKP1 gene. This alteration results from a T to A substitution at nucleotide position 205, causing the serine (S) at amino acid position 69 to be replaced by a threonine (T). 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.