NM_003680.4(YARS1):c.40A>T (p.Ile14Phe) AND Charcot-Marie-Tooth disease, dominant intermediate C

Clinical significance:Uncertain significance (Last evaluated: Nov 27, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001069984.1

Allele description [Variation Report for NM_003680.4(YARS1):c.40A>T (p.Ile14Phe)]

NM_003680.4(YARS1):c.40A>T (p.Ile14Phe)

Genes:
S100PBP:S100P binding protein [Gene - OMIM - HGNC]
YARS1:tyrosyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p35.1
Genomic location:
Preferred name:
NM_003680.4(YARS1):c.40A>T (p.Ile14Phe)
HGVS:
  • NC_000001.11:g.32817205T>A
  • NG_008408.1:g.5828A>T
  • NG_031988.1:g.4764T>A
  • NM_003680.3:c.40A>T
  • NM_003680.4:c.40A>TMANE SELECT
  • NP_003671.1:p.Ile14Phe
  • NP_003671.1:p.Ile14Phe
  • LRG_273t1:c.40A>T
  • LRG_273:g.5828A>T
  • LRG_273p1:p.Ile14Phe
  • NC_000001.10:g.33282806T>A
Protein change:
I14F
Links:
dbSNP: rs763337272
NCBI 1000 Genomes Browser:
rs763337272
Molecular consequence:
  • NM_003680.3:c.40A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003680.4:c.40A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Charcot-Marie-Tooth disease, dominant intermediate C (CMTDIC)
Synonyms:
CHARCOT-MARIE-TOOTH NEUROPATHY, DOMINANT INTERMEDIATE C
Identifiers:
MONDO: MONDO:0012012; MedGen: C1842237; OMIM: 608323

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001235189Invitaecriteria provided, single submitter
Uncertain significance
(Nov 27, 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, SCV001235189.2

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

Description

This sequence change replaces isoleucine with phenylalanine at codon 14 of the YARS protein (p.Ile14Phe). The isoleucine residue is highly conserved and there is a small physicochemical difference between isoleucine and phenylalanine. This variant is present in population databases (rs763337272, ExAC 0.006%). This variant has not been reported in the literature in individuals with YARS-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: Probably Damaging; Align-GVGD: Class C1). 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. 5

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

Last Updated: Nov 27, 2021

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