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NM_001136472.2(LITAF):c.268C>T (p.Arg90Cys) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 14, 2023
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:
RCV003155313.1

Allele description [Variation Report for NM_001136472.2(LITAF):c.268C>T (p.Arg90Cys)]

NM_001136472.2(LITAF):c.268C>T (p.Arg90Cys)

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.268C>T (p.Arg90Cys)
HGVS:
  • NC_000016.10:g.11553642G>A
  • NG_009008.1:g.38309C>T
  • NM_001136472.2:c.268C>TMANE SELECT
  • NM_001136473.1:c.268C>T
  • NM_004862.4:c.268C>T
  • NP_001129944.1:p.Arg90Cys
  • NP_001129945.1:p.Arg90Cys
  • NP_004853.2:p.Arg90Cys
  • NP_004853.2:p.Arg90Cys
  • LRG_253t1:c.268C>T
  • LRG_253:g.38309C>T
  • LRG_253p1:p.Arg90Cys
  • NC_000016.9:g.11647498G>A
  • NM_004862.3:c.268C>T
  • NR_024320.2:n.402C>T
Protein change:
R90C
Links:
dbSNP: rs375665454
NCBI 1000 Genomes Browser:
rs375665454
Molecular consequence:
  • NM_001136472.2:c.268C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136473.1:c.268C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004862.4:c.268C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_024320.2:n.402C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003844707Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Feb 14, 2023) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Comprehensive genetic sequence and copy number analysis for Charcot-Marie-Tooth disease in a Canadian cohort of 2517 patients.

Volodarsky M, Kerkhof J, Stuart A, Levy M, Brady LI, Tarnopolsky M, Lin H, Ainsworth P, Sadikovic B.

J Med Genet. 2021 Apr;58(4):284-288. doi: 10.1136/jmedgenet-2019-106641. Epub 2020 May 6.

PubMed [citation]
PMID:
32376792

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003844707.1

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

Description

Variant summary: LITAF c.268C>T (p.Arg90Cys) results in a non-conservative amino acid change located in the LPS-induced tumour necrosis factor alpha factor domain (IPR006629) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 9.6e-05 in 251016 control chromosomes. c.268C>T has been reported in the literature in individuals affected with Charcot-Marie Disease Type 1C (Volodarsky_2020). This report does not provide unequivocal conclusions about association of the variant with Charcot-Marie Disease Type 1C. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two ClinVar submitters have submitted clinical-significance assessments for this variant to ClinVar after 2014. All laboratories classified the variant as uncertain significance (n=2). Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Feb 28, 2024