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NM_001182.5(ALDH7A1):c.247G>A (p.Ala83Thr) AND Pyridoxine-dependent epilepsy

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 2, 2021
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:
RCV000703644.5

Allele description

NM_001182.5(ALDH7A1):c.247G>A (p.Ala83Thr)

Gene:
ALDH7A1:aldehyde dehydrogenase 7 family member A1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q23.2
Genomic location:
Preferred name:
NM_001182.5(ALDH7A1):c.247G>A (p.Ala83Thr)
HGVS:
  • NC_000005.10:g.126592729C>T
  • NG_008600.2:g.7662G>A
  • NM_001182.5:c.247G>AMANE SELECT
  • NM_001201377.2:c.163G>A
  • NM_001202404.2:c.247G>A
  • NP_001173.2:p.Ala83Thr
  • NP_001188306.1:p.Ala55Thr
  • NP_001189333.2:p.Ala83Thr
  • NC_000005.9:g.125928421C>T
  • NM_001182.4:c.247G>A
Protein change:
A55T
Links:
dbSNP: rs1561672611
NCBI 1000 Genomes Browser:
rs1561672611
Molecular consequence:
  • NM_001182.5:c.247G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001201377.2:c.163G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202404.2:c.247G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Pyridoxine-dependent epilepsy (EPEO4)
Synonyms:
Pyridoxine dependency; Pyridoxine dependency with seizures; Vitamin B6-dependent seizures; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009945; MedGen: C1849508; Orphanet: 3006; OMIM: 266100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000832553Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 2, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000832553.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces alanine with threonine at codon 83 of the ALDH7A1 protein (p.Ala83Thr). The alanine residue is moderately conserved and there is a small physicochemical difference between alanine and threonine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with ALDH7A1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 28, 2023