3-136316958-AT-ATT
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000532.5(PCCB):c.990dupT(p.Glu331fs) variant causes a frameshift, stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,614,080 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000532.5 frameshift, stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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PCCB | NM_000532.5 | c.990dupT | p.Glu331fs | frameshift_variant, stop_gained | Exon 10 of 15 | ENST00000251654.9 | NP_000523.2 | |
PCCB | NM_001178014.2 | c.1050dupT | p.Glu351fs | frameshift_variant, stop_gained | Exon 11 of 16 | NP_001171485.1 | ||
PCCB | XM_011512873.2 | c.990dupT | p.Glu331fs | frameshift_variant, stop_gained | Exon 10 of 11 | XP_011511175.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152110Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251448Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135894
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461852Hom.: 0 Cov.: 33 AF XY: 0.0000358 AC XY: 26AN XY: 727236
GnomAD4 genome AF: 0.000322 AC: 49AN: 152228Hom.: 0 Cov.: 31 AF XY: 0.000242 AC XY: 18AN XY: 74426
ClinVar
Submissions by phenotype
Propionic acidemia Pathogenic:11
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This sequence change creates a premature translational stop signal (p.Glu331*) in the PCCB gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PCCB are known to be pathogenic (PMID: 15464417). This variant is present in population databases (rs763069936, gnomAD 0.1%). This premature translational stop signal has been observed in individuals with propionic aciduria (PMID: 12559849, 22033733, 23430860, 24516753). ClinVar contains an entry for this variant (Variation ID: 167423). For these reasons, this variant has been classified as Pathogenic. -
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Variant summary: The PCCB c.990dupT (p.Glu331X) variant results in a premature termination codon, predicted to cause a truncated or absent PCCB protein due to nonsense mediated decay, which are commonly known mechanisms for disease.This variant was found in 6/121406 control chromosomes at a frequency of 0.0000494, which does not exceed the estimated maximal expected allele frequency of a pathogenic PCCB variant (0.0025). Multiple publications have cited the variant in affected compound heterozygote and homozygote individuals. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. -
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This nonsense variant found in exon 11 of 16 is predicted to result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (NMD). This variant has been previously reported as both a compound heterozygous and homozygous change in patients with propionic acidemia (MIM#: 606054; PMID: 12559849, 22033733, 23430860, 24516753). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.0008% (25/282848) and thus is presumed to be rare. Based on the available evidence, the c.1050dup (p.Glu351Ter) variant is classified as Pathogenic. -
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not provided Pathogenic:2
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 22033733, 24516753, 24059531, 23430860, 20549364, 12559849, 30705822, 31916709) -
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PCCB-related disorder Pathogenic:1
The PCCB c.990dupT variant is predicted to result in premature protein termination (p.Glu331*). This variant has been reported in the compound heterozygous state with a second pathogenic variant or in the homozygous state in unrelated individuals with propionic acidemia (Pérez et al. 2003. PubMed ID: 12559849; Ali et al. 2011. PubMed ID: 21483992; Al-Hamed et al. 2019. PubMed ID: 30705822). Analysis of propionyl-CoA carboxylase (PCC) activity in skin fibroblasts from a patient who was compound heterozygous for this variant and a second pathogenic variant (c.1228C>T, p.Arg410Trp) revealed that together, these two variants nearly abolished the enzyme activity (Pérez-Cerdá et al. 2003. PubMed ID: 12757933). This variant is reported in 0.10% of alleles in individuals of African descent in gnomAD. Nonsense variants in PCCB are expected to be pathogenic. This variant is interpreted as pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at