NM_000382.3(ALDH3A2):c.1339A>G (p.Lys447Glu) AND ALDH3A2-related disorder

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Oct 17, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003420747.4

Allele description [Variation Report for NM_000382.3(ALDH3A2):c.1339A>G (p.Lys447Glu)]

NM_000382.3(ALDH3A2):c.1339A>G (p.Lys447Glu)

Gene:

ALDH3A2:aldehyde dehydrogenase 3 family member A2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p11.2

Genomic location:

Preferred name:

NM_000382.3(ALDH3A2):c.1339A>G (p.Lys447Glu)

HGVS:

NC_000017.11:g.19671852A>G
NG_007095.2:g.28102A>G
NM_000382.3:c.1339A>GMANE SELECT
NM_001031806.2:c.1339A>G
NM_001369136.1:c.1339A>G
NM_001369137.2:c.1339A>G
NM_001369138.2:c.1339A>G
NM_001369139.1:c.1339A>G
NM_001369146.2:c.1208-3706A>G
NM_001369148.2:c.760A>G
NP_000373.1:p.Lys447Glu
NP_001026976.1:p.Lys447Glu
NP_001356065.1:p.Lys447Glu
NP_001356066.1:p.Lys447Glu
NP_001356067.1:p.Lys447Glu
NP_001356068.1:p.Lys447Glu
NP_001356077.1:p.Lys254Glu
NC_000017.10:g.19575165A>G
NM_000382.2:c.1339A>G

Protein change:

K254E

Molecular consequence:

NM_001369146.2:c.1208-3706A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000382.3:c.1339A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001031806.2:c.1339A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001369136.1:c.1339A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001369137.2:c.1339A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001369138.2:c.1339A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001369139.1:c.1339A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001369148.2:c.760A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: ALDH3A2-related disorder
Synonyms:: ALDH3A2-related condition
Identifiers:

Recent activity

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Danio rerio strain Tuebingen, whole genome shotgun sequencing, Contig_0101319, w...
Danio rerio strain Tuebingen, whole genome shotgun sequencing, Contig_0101319, whole genome shotgun sequence
gi|296636660|emb|CABZ01093034.1|

Nucleotide
PREDICTED: Thrips palmi dnaJ homolog subfamily B member 6 (LOC117646022), transc...
PREDICTED: Thrips palmi dnaJ homolog subfamily B member 6 (LOC117646022), transcript variant X3, mRNA
gi|1841826284|ref|XM_034386647.1|

Nucleotide
PREDICTED: Thrips palmi dnaJ homolog subfamily B member 6 (LOC117646022), transc...
PREDICTED: Thrips palmi dnaJ homolog subfamily B member 6 (LOC117646022), transcript variant X5, mRNA
gi|1841826288|ref|XM_034386650.1|

Nucleotide
Streptomyces sp. TRM46602 16S ribosomal RNA gene, partial sequence
Streptomyces sp. TRM46602 16S ribosomal RNA gene, partial sequence
gi|408683814|gb|JX244147.1|

Nucleotide
transposase (plasmid) [Pseudomonas luteola]
transposase (plasmid) [Pseudomonas luteola]
gi|1751081787|gnl|PRJNA231221|FOB45 5|gb|QEU26804.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004106749	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 17, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004106749

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 17, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004106749.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The ALDH3A2 c.1339A>G variant is predicted to result in the amino acid substitution p.Lys447Glu. This variant has been reported in the homozygous and compound heterozygous states in patients with Sjogren-Larsson syndrome and was found to reduce enzymatic activity to ~1% of wild-type in an in vitro functional assay (Rizzo et al 1999. PubMed ID: 10577908; Tachibana et al. 2012. PubMed ID: 21713441; Arai et al. 2022. PubMed ID: 35973883). This variant is reported in 0.0054% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/17-19575165-A-G). This variant is interpreted as likely pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Aug 4, 2024

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