rs1555728990
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001289104.2(PRKCSH):āc.1416T>Gā(p.Tyr472Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,584 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 Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001289104.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKCSH | NM_001289104.2 | c.1416T>G | p.Tyr472Ter | stop_gained | 16/18 | ENST00000677123.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKCSH | ENST00000677123.1 | c.1416T>G | p.Tyr472Ter | stop_gained | 16/18 | NM_001289104.2 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461584Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727096
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Polycystic liver disease 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at