rs750815894
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000288.4(PEX7):āc.733A>Gā(p.Ile245Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000276 in 1,449,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_000288.4 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 |
---|---|---|---|---|---|---|---|---|
PEX7 | NM_000288.4 | c.733A>G | p.Ile245Val | missense_variant | 7/10 | ENST00000318471.5 | NP_000279.1 | |
PEX7 | NM_001410945.1 | c.619A>G | p.Ile207Val | missense_variant | 7/10 | NP_001397874.1 | ||
PEX7 | XM_006715502.3 | c.439A>G | p.Ile147Val | missense_variant | 4/7 | XP_006715565.1 | ||
PEX7 | XM_047418874.1 | c.526+23808A>G | intron_variant | XP_047274830.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PEX7 | ENST00000318471.5 | c.733A>G | p.Ile245Val | missense_variant | 7/10 | 1 | NM_000288.4 | ENSP00000315680.3 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152212Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251392Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135876
GnomAD4 exome AF: 0.00000276 AC: 4AN: 1449436Hom.: 0 Cov.: 27 AF XY: 0.00000277 AC XY: 2AN XY: 721798
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74362
ClinVar
Submissions by phenotype
Peroxisome biogenesis disorder 9B Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 245 of the PEX7 protein (p.Ile245Val). This variant is present in population databases (rs750815894, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with PEX7-related conditions. ClinVar contains an entry for this variant (Variation ID: 1504254). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at