NM_000382.3(ALDH3A2):c.798+1del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 20, 2023
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:: RCV001231409.6

Allele description [Variation Report for NM_000382.3(ALDH3A2):c.798+1del]

NM_000382.3(ALDH3A2):c.798+1del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

17p11.2

Genomic location:

Preferred name:

NM_000382.3(ALDH3A2):c.798+1del

HGVS:

NC_000017.11:g.19657863del
NG_007095.2:g.14113del
NM_000382.3:c.798+1delMANE SELECT
NM_001031806.2:c.798+1del
NM_001369136.1:c.798+1del
NM_001369137.2:c.798+1del
NM_001369138.2:c.798+1del
NM_001369139.1:c.798+1del
NM_001369146.2:c.798+1del
NM_001369148.2:c.219+1del
NC_000017.10:g.19561175del
NC_000017.10:g.19561176del
NM_000382.2:c.798+1del
NM_000382.2:c.798+1delG
NM_000382.3:c.798+1delGMANE SELECT

Links:

dbSNP: rs757359379

NCBI 1000 Genomes Browser:

rs757359379

Molecular consequence:

NM_000382.3:c.798+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001031806.2:c.798+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001369136.1:c.798+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001369137.2:c.798+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001369138.2:c.798+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001369139.1:c.798+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001369146.2:c.798+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001369148.2:c.219+1del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Schizosaccharomyces pombe
Schizosaccharomyces pombe
Genome-wide Profiling of DNA Replication Timing in pombe.

BioProject
Uncultured alpha proteobacterium GT40-3 16S ribosomal RNA gene, partial sequence
Uncultured alpha proteobacterium GT40-3 16S ribosomal RNA gene, partial sequence
gi|8050781|gb|AF256034.1|

Nucleotide
Enterobacter bugandensis strain ECH7 DnaJ (dnaJ) gene, partial cds
Enterobacter bugandensis strain ECH7 DnaJ (dnaJ) gene, partial cds
gi|1886431082|gb|MT665014.1|

Nucleotide
Pseudomonas sp. YXE2-e 16S ribosomal RNA gene, partial sequence
Pseudomonas sp. YXE2-e 16S ribosomal RNA gene, partial sequence
gi|334855450|gb|JF701974.1|

Nucleotide
Psychotria ndhF-rpl32 intergenic spacer, partial sequence; chloroplast.
Psychotria ndhF-rpl32 intergenic spacer, partial sequence; chloroplast.
PopSet: 347983082

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001403929	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 20, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 16199547, 10854114, 30157790, 10577908, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001403929

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 20, 2023)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

RNA-based mutation screening in German families with Sjögren-Larsson syndrome.

Kraus C, Braun-Quentin C, Ballhausen WG, Pfeiffer RA.

Eur J Hum Genet. 2000 Apr;8(4):299-306.

PubMed [citation]

PMID:: 10854114

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001403929.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change affects a splice site in intron 5 of the ALDH3A2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ALDH3A2 are known to be pathogenic (PMID: 10577908, 10854114). This variant is present in population databases (rs757359379, gnomAD 0.006%). Disruption of this splice site has been observed in individuals with Sj√∂gren-Larsson syndrome (PMID: 10577908, 30157790). ClinVar contains an entry for this variant (Variation ID: 371195). Studies have shown that disruption of this splice site is associated with altered splicing resulting in multiple RNA products (PMID: 10577908). For these reasons, this variant has been classified as 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: Oct 8, 2024

ClinVar

Relating variation to medicine