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NM_001136472.2(LITAF):c.233C>T (p.Thr78Met) AND Charcot-Marie-Tooth disease type 1C

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 7, 2021
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:
RCV001903691.6

Allele description [Variation Report for NM_001136472.2(LITAF):c.233C>T (p.Thr78Met)]

NM_001136472.2(LITAF):c.233C>T (p.Thr78Met)

Gene:
LITAF:lipopolysaccharide induced TNF factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.13
Genomic location:
Preferred name:
NM_001136472.2(LITAF):c.233C>T (p.Thr78Met)
HGVS:
  • NC_000016.10:g.11553677G>A
  • NG_009008.1:g.38274C>T
  • NM_001136472.2:c.233C>TMANE SELECT
  • NM_001136473.1:c.233C>T
  • NM_004862.4:c.233C>T
  • NP_001129944.1:p.Thr78Met
  • NP_001129945.1:p.Thr78Met
  • NP_004853.2:p.Thr78Met
  • LRG_253t1:c.233C>T
  • LRG_253:g.38274C>T
  • LRG_253p1:p.Thr78Met
  • NC_000016.9:g.11647533G>A
  • NM_004862.3:c.233C>T
  • NR_024320.2:n.367C>T
Protein change:
T78M
Links:
dbSNP: rs1228516620
NCBI 1000 Genomes Browser:
rs1228516620
Molecular consequence:
  • NM_001136472.2:c.233C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136473.1:c.233C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004862.4:c.233C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_024320.2:n.367C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Charcot-Marie-Tooth disease type 1C
Synonyms:
CMT, SLOW NERVE CONDUCTION TYPE C; HMSN IC; CMT 1C; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010995; MedGen: C0270913; Orphanet: 101083; OMIM: 601098

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002173579Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 7, 2021) 		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, SCV002173579.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). This variant has not been reported in the literature in individuals with LITAF-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces threonine with methionine at codon 78 of the LITAF protein (p.Thr78Met). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and methionine.

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

Last Updated: Sep 29, 2024