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NM_001199107.2(TBC1D24):c.343C>T (p.Arg115Cys) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 21, 2024
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:
RCV001058657.12

Allele description [Variation Report for NM_001199107.2(TBC1D24):c.343C>T (p.Arg115Cys)]

NM_001199107.2(TBC1D24):c.343C>T (p.Arg115Cys)

Gene:
TBC1D24:TBC1 domain family member 24 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_001199107.2(TBC1D24):c.343C>T (p.Arg115Cys)
Other names:
p.R115C:CGC>TGC; p.Arg115Cys
HGVS:
  • NC_000016.10:g.2496491C>T
  • NG_028170.1:g.26346C>T
  • NM_001199107.2:c.343C>TMANE SELECT
  • NM_020705.3:c.343C>T
  • NP_001186036.1:p.Arg115Cys
  • NP_065756.1:p.Arg115Cys
  • NC_000016.9:g.2546492C>T
  • NM_001199107.1:c.343C>T
  • NM_020705.2:c.343C>T
Protein change:
R115C
Links:
dbSNP: rs372531999
NCBI 1000 Genomes Browser:
rs372531999
Molecular consequence:
  • NM_001199107.2:c.343C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020705.3:c.343C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Developmental and epileptic encephalopathy, 1 (DEE1)
Synonyms:
INFANTILE SPASM SYNDROME, X-LINKED 1; X-linked infantile spasms; West's syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010632; MedGen: C3463992; OMIM: 308350
Name:
Autosomal dominant nonsyndromic hearing loss 65
Synonyms:
Deafness, autosomal dominant 65
Identifiers:
MONDO: MONDO:0014470; MedGen: C3892048; Orphanet: 90635; OMIM: 616044
Name:
Caused by mutation in the TBC1 domain family, member 24
Identifiers:
MedGen: CN236805

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001223244Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 21, 2024) 		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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001223244.5

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

Description

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 115 of the TBC1D24 protein (p.Arg115Cys). This variant is present in population databases (rs372531999, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with TBC1D24-related conditions. ClinVar contains an entry for this variant (Variation ID: 207496). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TBC1D24 protein function with a negative predictive value of 80%. 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: Apr 20, 2024