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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uncharacterized protein BCR37DRAFT_384835 [Protomyces lactucae-debilis]
uncharacterized protein BCR37DRAFT_384835 [Protomyces lactucae-debilis]
gi|2027897785|ref|XP_040721792.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000963567	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 2, 2018)	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

SCV000963567

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 2, 2018)

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

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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

#	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: Sep 29, 2024

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