17-19648999-C-T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_000382.3(ALDH3A2):c.28C>T(p.Gln10*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000419 in 1,433,450 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000382.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000514 AC: 1AN: 194412Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 105310
GnomAD4 exome AF: 0.00000419 AC: 6AN: 1433450Hom.: 0 Cov.: 30 AF XY: 0.00000282 AC XY: 2AN XY: 710456
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Sjögren-Larsson syndrome Pathogenic:2Uncertain:1
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The ALDH3A2 c.28C>T (p.Gln10Ter) variant is a stop-gained variant that is predicted to result in premature termination of the protein and has been reported in a heterozygous state in a Spanish individual with Sjogren-Larsson syndrome (Rizzo et al. 1999). Cultured skin fibroblasts from this individual were shown to be deficient in FALDH, but the individual's full genotype was not clearly reported. In addition, Sanabria and Coco (2011) report the p.Gln10Ter variant in a heterozygous state in two siblings with Sjogren-Larsson syndrome who were also heterozygous for an in-frame deletion variant; the phase of the variants in these individuals was not reported. Control data are unavailable for the p.Gln10Ter variant, which is reported at a frequency of 0.000383 in the East Asian population of the Exome Aggregation Consortium. However, this frequency is based on only one allele in a region of poor sequence coverage. Based on the limited evidence available and the potential impact of stop-gained variants, the p.Gln10Ter variant is classified as a variant of unknown significance but suspicious for pathogenicity for Sjogren-Larsson syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
not provided Pathogenic:1
This sequence change creates a premature translational stop signal (p.Gln10*) in the ALDH3A2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ALDH3A2 are known to be pathogenic (PMID: 10577908, 10854114). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This premature translational stop signal has been observed in individual(s) with Sjogren-Larsson syndrome (PMID: 10577908, 21968182). ClinVar contains an entry for this variant (Variation ID: 188833). For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at