NM_001085411.3(NADK2):c.703C>T (p.Pro235Ser) AND Progressive encephalopathy with leukodystrophy due to DECR deficiency

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 10, 2022
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:: RCV001956714.5

Allele description

NM_001085411.3(NADK2):c.703C>T (p.Pro235Ser)

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.703C>T (p.Pro235Ser)

HGVS:

NC_000005.10:g.36217826G>A
NG_041784.1:g.29454C>T
NM_001085411.3:c.703C>TMANE SELECT
NM_001287340.2:c.214C>T
NM_001287341.2:c.214C>T
NM_153013.5:c.214C>T
NP_001078880.1:p.Pro235Ser
NP_001274269.1:p.Pro72Ser
NP_001274270.1:p.Pro72Ser
NP_694558.1:p.Pro72Ser
NC_000005.9:g.36217928G>A

Protein change:

P235S

Links:

dbSNP: rs2112132418

NCBI 1000 Genomes Browser:

rs2112132418

Molecular consequence:

NM_001085411.3:c.703C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001287340.2:c.214C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001287341.2:c.214C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_153013.5:c.214C>T - missense variant - [Sequence Ontology: SO:0001583]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002250029	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 10, 2022)	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

SCV002250029

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 10, 2022)

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 Invitae, SCV002250029.3

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

Description

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. 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: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C25"). ClinVar contains an entry for this variant (Variation ID: 1463792). This variant has not been reported in the literature in individuals affected with NADK2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 235 of the NADK2 protein (p.Pro235Ser).

#	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: Feb 28, 2024

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