rs786204417
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_000288.4(PEX7):c.400G>A(p.Asp134Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000344 in 1,452,342 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D134V) has been classified as Uncertain significance.
Frequency
Consequence
NM_000288.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX7 | NM_000288.4 | c.400G>A | p.Asp134Asn | missense_variant | 4/10 | ENST00000318471.5 | |
PEX7 | NM_001410945.1 | c.286G>A | p.Asp96Asn | missense_variant | 4/10 | ||
PEX7 | XM_047418874.1 | c.400G>A | p.Asp134Asn | missense_variant | 4/6 | ||
PEX7 | XM_006715502.3 | c.339+19206G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX7 | ENST00000318471.5 | c.400G>A | p.Asp134Asn | missense_variant | 4/10 | 1 | NM_000288.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251418Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135880
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1452342Hom.: 0 Cov.: 29 AF XY: 0.00000415 AC XY: 3AN XY: 723170
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Rhizomelic chondrodysplasia punctata type 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | literature only | Counsyl | Mar 02, 2014 | - - |
Peroxisome biogenesis disorder 9B Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Sep 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at