1-225921254-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PM5PP3_Moderate
The NM_013328.4(PYCR2):c.751C>A(p.Arg251Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R251C) has been classified as Pathogenic.
Frequency
Consequence
NM_013328.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PYCR2 | NM_013328.4 | c.751C>A | p.Arg251Ser | missense_variant | Exon 6 of 7 | ENST00000343818.11 | NP_037460.2 | |
PYCR2 | NM_001271681.2 | c.529C>A | p.Arg177Ser | missense_variant | Exon 5 of 6 | NP_001258610.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PYCR2 | ENST00000343818.11 | c.751C>A | p.Arg251Ser | missense_variant | Exon 6 of 7 | 1 | NM_013328.4 | ENSP00000342502.6 | ||
ENSG00000255835 | ENST00000432920.2 | c.529C>A | p.Arg177Ser | missense_variant | Exon 5 of 8 | 2 | ENSP00000414068.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at