rs74315402
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PS1PM2PP3_Moderate
The ENST00000379440.9(PRNP):c.350C>T(p.Ala117Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar. Synonymous variant affecting the same amino acid position (i.e. A117A) has been classified as Benign.
Frequency
Consequence
ENST00000379440.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRNP | NM_000311.5 | c.350C>T | p.Ala117Val | missense_variant | 2/2 | ENST00000379440.9 | NP_000302.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRNP | ENST00000379440.9 | c.350C>T | p.Ala117Val | missense_variant | 2/2 | 1 | NM_000311.5 | ENSP00000368752 | P1 | |
PRNP | ENST00000424424.2 | c.350C>T | p.Ala117Val | missense_variant | 2/2 | 1 | ENSP00000411599 | P1 | ||
PRNP | ENST00000430350.2 | c.350C>T | p.Ala117Val | missense_variant | 2/2 | 1 | ENSP00000399376 | P1 | ||
PRNP | ENST00000457586.2 | c.350C>T | p.Ala117Val | missense_variant | 2/2 | 1 | ENSP00000415284 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 02, 2017 | - - |
Gerstmann-Straussler-Scheinker syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 1999 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at