NM_001182.5(ALDH7A1):c.1565+15T>C AND Pyridoxine-dependent epilepsy

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Aug 25, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002063426.6

Allele description

NM_001182.5(ALDH7A1):c.1565+15T>C

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.1565+15T>C

HGVS:

NC_000005.10:g.126546309A>G
NG_008600.2:g.54082T>C
NM_001182.5:c.1565+15T>CMANE SELECT
NM_001201377.2:c.1481+15T>C
NM_001202404.2:c.1373+15T>C
NC_000005.9:g.125882001A>G
NM_001182.4:c.1565+15T>C

Links:

dbSNP: rs375505703

NCBI 1000 Genomes Browser:

rs375505703

Molecular consequence:

NM_001182.5:c.1565+15T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001201377.2:c.1481+15T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001202404.2:c.1373+15T>C - intron variant - [Sequence Ontology: SO:0001627]

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

Recent activity

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Homo sapiens von-Hippel-Lindau-like protein (VLP) mRNA, complete cds
Homo sapiens von-Hippel-Lindau-like protein (VLP) mRNA, complete cds
gi|44895312|gb|AY494836.1|

Nucleotide
enolase 4 isoform X3 [Homo sapiens]
enolase 4 isoform X3 [Homo sapiens]
gi|2217277248|ref|XP_047281184.1|

Protein
LETM1 domain-containing protein LETM2, mitochondrial isoform 7 precursor [Homo s...
LETM1 domain-containing protein LETM2, mitochondrial isoform 7 precursor [Homo sapiens]
gi|1388591311|ref|NP_001350133.1|

Protein
LETM1 domain-containing protein LETM2, mitochondrial isoform X1 [Homo sapiens]
LETM1 domain-containing protein LETM2, mitochondrial isoform X1 [Homo sapiens]
gi|2462617808|ref|XP_054215757.1|

Protein
PREDICTED: Homo sapiens N-myristoyltransferase 2 (NMT2), transcript variant X4, ...
PREDICTED: Homo sapiens N-myristoyltransferase 2 (NMT2), transcript variant X4, mRNA
gi|2217279462|ref|XM_047426019.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002335120	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Aug 25, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004049995	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 11, 2023)	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

SCV002335120

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Aug 25, 2023)

germline

clinical testing

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

SCV004049995

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Apr 11, 2023)

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
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical 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

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 Invitae, SCV002335120.3

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

#	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

From Genome-Nilou Lab, SCV004049995.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

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