NM_000382.3:c.1A>G
Variant names:
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_000382.3(ALDH3A2):c.1A>G(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000209 in 1,434,150 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 (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
ALDH3A2
NM_000382.3 start_lost
NM_000382.3 start_lost
Scores
3
9
4
Clinical Significance
Conservation
PhyloP100: 1.28
Genes affected
ALDH3A2 (HGNC:403): (aldehyde dehydrogenase 3 family member A2) Aldehyde dehydrogenase isozymes are thought to play a major role in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. This gene product catalyzes the oxidation of long-chain aliphatic aldehydes to fatty acid. Mutations in the gene cause Sjogren-Larsson syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
PVS1
Start lost variant, next in-frame start position is after 5 pathogenic variants. Next in-frame start position is after 33 codons. Genomic position: 19649068. Lost 0.067 part of the original CDS.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-19648972-A-G is Pathogenic according to our data. Variant chr17-19648972-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 551722.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000209 AC: 3AN: 1434150Hom.: 0 Cov.: 30 AF XY: 0.00000281 AC XY: 2AN XY: 710838
GnomAD4 exome
AF:
AC:
3
AN:
1434150
Hom.:
Cov.:
30
AF XY:
AC XY:
2
AN XY:
710838
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
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Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
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Gnomad4 FIN exome
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Gnomad4 NFE exome
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Gnomad4 OTH exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Sjögren-Larsson syndrome Pathogenic:1
May 02, 2017
Counsyl
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
.;T;.;.;T;.;T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;.;.;D;.;.;D;.
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
D
PROVEAN
Benign
N;.;.;.;N;.;N;N;.
REVEL
Uncertain
Sift
Uncertain
D;.;.;.;D;.;D;D;.
Sift4G
Uncertain
D;D;D;T;D;T;D;T;D
Polyphen
0.97, 0.99
.;.;.;.;D;D;D;D;D
Vest4
0.40, 0.68, 0.68, 0.42, 0.68, 0.73, 0.67
MutPred
Gain of methylation at R6 (P = 0.1593);Gain of methylation at R6 (P = 0.1593);Gain of methylation at R6 (P = 0.1593);Gain of methylation at R6 (P = 0.1593);Gain of methylation at R6 (P = 0.1593);Gain of methylation at R6 (P = 0.1593);Gain of methylation at R6 (P = 0.1593);Gain of methylation at R6 (P = 0.1593);Gain of methylation at R6 (P = 0.1593);
MVP
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.