rs281875318
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PP3_ModeratePP5
The NM_006907.4(PYCR1):c.769G>A(p.Ala257Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000384 in 1,612,774 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A257V) has been classified as Uncertain significance.
Frequency
Consequence
NM_006907.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PYCR1 | NM_006907.4 | c.769G>A | p.Ala257Thr | missense_variant | 6/7 | ENST00000329875.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYCR1 | ENST00000329875.13 | c.769G>A | p.Ala257Thr | missense_variant | 6/7 | 1 | NM_006907.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248344Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134826
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1460544Hom.: 0 Cov.: 33 AF XY: 0.0000317 AC XY: 23AN XY: 726518
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
not provided Uncertain:1Other:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 257 of the PYCR1 protein (p.Ala257Thr). This variant is present in population databases (rs281875318, gnomAD 0.01%). This missense change has been observed in individuals with cutis laxa (PMID: 19648921, 30450527). ClinVar contains an entry for this variant (Variation ID: 29863). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PYCR1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
not provided, no classification provided | literature only | UniProtKB/Swiss-Prot | - | - - |
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2018 | - - |
PYCR1-related de Barsy syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2009 | - - |
Wiedemann-Rautenstrauch-like progeroid syndrome Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at