rs121434232
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_021628.3(ALOXE3):c.1498G>T(p.Val500Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V500G) has been classified as Uncertain significance.
Frequency
Consequence
NM_021628.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALOXE3 | NM_021628.3 | c.1498G>T | p.Val500Phe | missense_variant | 12/16 | ENST00000448843.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALOXE3 | ENST00000448843.7 | c.1498G>T | p.Val500Phe | missense_variant | 12/16 | 1 | NM_021628.3 | P1 | |
ALOXE3 | ENST00000380149.6 | c.1498G>T | p.Val500Phe | missense_variant | 11/15 | 1 | P1 | ||
ALOXE3 | ENST00000318227.4 | c.1498G>T | p.Val500Phe | missense_variant | 12/16 | 2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Autosomal recessive congenital ichthyosis 3 Pathogenic:2
Pathogenic, no assertion criteria provided | clinical testing | Institute for Human Genetics, University Medical Center Freiburg | Jan 07, 2021 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2002 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at