NM_006096.4(NDRG1):c.488T>C (p.Ile163Thr) AND Charcot-Marie-Tooth disease type 4

Clinical significance:Uncertain significance (Last evaluated: Jul 22, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001243503.1

Allele description [Variation Report for NM_006096.4(NDRG1):c.488T>C (p.Ile163Thr)]

NM_006096.4(NDRG1):c.488T>C (p.Ile163Thr)

Gene:
NDRG1:N-myc downstream regulated 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8q24.22
Genomic location:
Preferred name:
NM_006096.4(NDRG1):c.488T>C (p.Ile163Thr)
HGVS:
  • NC_000008.11:g.133256826A>G
  • NG_007943.1:g.45430T>C
  • NM_001135242.2:c.488T>C
  • NM_001258432.2:c.290T>C
  • NM_001258433.2:c.245T>C
  • NM_001374844.1:c.488T>C
  • NM_001374845.1:c.488T>C
  • NM_001374846.1:c.488T>C
  • NM_001374847.1:c.290T>C
  • NM_006096.4:c.488T>CMANE SELECT
  • NP_001128714.1:p.Ile163Thr
  • NP_001245361.1:p.Ile97Thr
  • NP_001245362.1:p.Ile82Thr
  • NP_001361773.1:p.Ile163Thr
  • NP_001361774.1:p.Ile163Thr
  • NP_001361775.1:p.Ile163Thr
  • NP_001361776.1:p.Ile97Thr
  • NP_006087.2:p.Ile163Thr
  • LRG_258t1:c.488T>C
  • LRG_258:g.45430T>C
  • NC_000008.10:g.134269069A>G
  • NM_006096.3:c.488T>C
Protein change:
I163T
Links:
dbSNP: rs748782766
NCBI 1000 Genomes Browser:
rs748782766
Molecular consequence:
  • NM_001135242.2:c.488T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258432.2:c.290T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258433.2:c.245T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374844.1:c.488T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374845.1:c.488T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374846.1:c.488T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374847.1:c.290T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006096.4:c.488T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Charcot-Marie-Tooth disease type 4
Synonyms:
Charcot-Marie-Tooth, Type 4
Identifiers:
MONDO: MONDO:0018995; MedGen: C4082197

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001416669Invitaecriteria provided, single submitter
Uncertain significance
(Jul 22, 2019)
germlineclinical testing

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

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001416669.1

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

Description

This sequence change replaces isoleucine with threonine at codon 163 of the NDRG1 protein (p.Ile163Thr). The isoleucine residue is moderately conserved and there is a moderate physicochemical difference between isoleucine and threonine. This variant is present in population databases (rs748782766, ExAC 0.01%). This variant has not been reported in the literature in individuals with NDRG1-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: "Possibly Damaging"; Align-GVGD: "Class C0"). 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: Nov 27, 2021

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