rs73404416
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000248633.9(PEX1):c.1142C>T(p.Ala381Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,372 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A381D) has been classified as Likely benign.
Frequency
Consequence
ENST00000248633.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PEX1 | NM_000466.3 | c.1142C>T | p.Ala381Val | missense_variant | 5/24 | ENST00000248633.9 | NP_000457.1 | |
PEX1 | NM_001282677.2 | c.1142C>T | p.Ala381Val | missense_variant | 5/23 | NP_001269606.1 | ||
PEX1 | NM_001282678.2 | c.518C>T | p.Ala173Val | missense_variant | 5/24 | NP_001269607.1 | ||
PEX1 | XM_047420472.1 | c.1142C>T | p.Ala381Val | missense_variant | 5/23 | XP_047276428.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PEX1 | ENST00000248633.9 | c.1142C>T | p.Ala381Val | missense_variant | 5/24 | 1 | NM_000466.3 | ENSP00000248633 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251376Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135872
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461372Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727040
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Zellweger spectrum disorders Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 22, 2022 | This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 381 of the PEX1 protein (p.Ala381Val). This variant is present in population databases (rs73404416, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with PEX1-related conditions. 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 PEX1 protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at