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NM_001085411.3(NADK2):c.48G>A (p.Ala16=) AND Progressive encephalopathy with leukodystrophy due to DECR deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 2, 2018
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:
RCV000822751.7

Allele description [Variation Report for NM_001085411.3(NADK2):c.48G>A (p.Ala16=)]

NM_001085411.3(NADK2):c.48G>A (p.Ala16=)

Genes:
LOC129993801:ATAC-STARR-seq lymphoblastoid silent region 15972 [Gene]
NADK2:NAD kinase 2, mitochondrial [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5p13.2
Genomic location:
Preferred name:
NM_001085411.3(NADK2):c.48G>A (p.Ala16=)
HGVS:
  • NC_000005.10:g.36241751C>T
  • NG_041784.1:g.5529G>A
  • NM_001085411.3:c.48G>AMANE SELECT
  • NM_001287341.2:c.-190+345G>A
  • NM_153013.5:c.-190+345G>A
  • NP_001078880.1:p.Ala16=
  • NC_000005.9:g.36241853C>T
  • NM_001085411.2:c.48G>A
Links:
dbSNP: rs1579649598
NCBI 1000 Genomes Browser:
rs1579649598
Molecular consequence:
  • NM_001287341.2:c.-190+345G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_153013.5:c.-190+345G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001085411.3:c.48G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Progressive encephalopathy with leukodystrophy due to DECR deficiency
Synonyms:
2,4-Dienoyl-CoA reductase deficiency; Dienoyl-CoA reductase deficiency; 2,4-alpha dienoyl-CoA reductase deficiency
Identifiers:
MONDO: MONDO:0014464; MedGen: C1857252; Orphanet: 431361; OMIM: 616034

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000963567Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 2, 2018) 		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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000963567.4

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

Description

Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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. This variant has not been reported in the literature in individuals with NADK2-related disease. While this variant is not present in population databases, the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. This sequence change affects codon 16 of the NADK2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the NADK2 protein.

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

Last Updated: Sep 29, 2024