rs397514528
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PM5PP3_StrongPP5
The NM_001139.3(ALOX12B):c.2036G>T(p.Arg679Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,892 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R679H) has been classified as Pathogenic.
Frequency
Consequence
NM_001139.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALOX12B | NM_001139.3 | c.2036G>T | p.Arg679Leu | missense_variant | 15/15 | ENST00000647874.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALOX12B | ENST00000647874.1 | c.2036G>T | p.Arg679Leu | missense_variant | 15/15 | NM_001139.3 | P1 | ||
ALOX12B | ENST00000649809.1 | c.1100G>T | p.Arg367Leu | missense_variant | 8/8 | ||||
ALOX12B | ENST00000650441.1 | n.459G>T | non_coding_transcript_exon_variant | 4/4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727248
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Autosomal recessive congenital ichthyosis 2 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 | Oct 01, 2005 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at