rs150555106
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 5P and 9B. PM1PM5PP3BP4_StrongBP6BS2
The NM_000532.5(PCCB):c.815G>A(p.Arg272Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00196 in 1,614,118 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign 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. R272W) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000532.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCCB | NM_000532.5 | c.815G>A | p.Arg272Gln | missense_variant | 8/15 | ENST00000251654.9 | |
PCCB | NM_001178014.2 | c.875G>A | p.Arg292Gln | missense_variant | 9/16 | ||
PCCB | XM_011512873.2 | c.815G>A | p.Arg272Gln | missense_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCCB | ENST00000251654.9 | c.815G>A | p.Arg272Gln | missense_variant | 8/15 | 1 | NM_000532.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00167 AC: 254AN: 152174Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00195 AC: 491AN: 251470Hom.: 2 AF XY: 0.00206 AC XY: 280AN XY: 135908
GnomAD4 exome AF: 0.00199 AC: 2910AN: 1461824Hom.: 6 Cov.: 32 AF XY: 0.00199 AC XY: 1447AN XY: 727222
GnomAD4 genome AF: 0.00167 AC: 255AN: 152294Hom.: 1 Cov.: 32 AF XY: 0.00146 AC XY: 109AN XY: 74466
ClinVar
Submissions by phenotype
Propionic acidemia Uncertain:4Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 06, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | May 18, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 23, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 10, 2020 | - - |
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 20, 2021 | This variant is associated with the following publications: (PMID: 25851414) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 02, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | PCCB: PM5, BS1, BS2 - |
PCCB-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 20, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at