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NM_024577.4(SH3TC2):c.1942C>T (p.Arg648Trp) AND Hereditary motor and sensory neuropathy

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 24, 2019
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:
RCV001030761.5

Allele description [Variation Report for NM_024577.4(SH3TC2):c.1942C>T (p.Arg648Trp)]

NM_024577.4(SH3TC2):c.1942C>T (p.Arg648Trp)

Gene:
SH3TC2:SH3 domain and tetratricopeptide repeats 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q32
Genomic location:
Preferred name:
NM_024577.4(SH3TC2):c.1942C>T (p.Arg648Trp)
Other names:
p.Arg648Trp
HGVS:
  • NC_000005.10:g.149027790G>A
  • NG_007947.2:g.40385C>T
  • NM_024577.4:c.1942C>TMANE SELECT
  • NP_078853.2:p.Arg648Trp
  • NP_078853.2:p.Arg648Trp
  • LRG_269t1:c.1942C>T
  • LRG_269:g.40385C>T
  • LRG_269p1:p.Arg648Trp
  • NC_000005.9:g.148407353G>A
  • NM_024577.3:c.1942C>T
Protein change:
R648W
Links:
dbSNP: rs537049075
NCBI 1000 Genomes Browser:
rs537049075
Molecular consequence:
  • NM_024577.4:c.1942C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Hereditary motor and sensory neuropathy
Identifiers:
MONDO: MONDO:0015358; MedGen: C0027888

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001190224Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Dec 24, 2019) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology, SCV001190224.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)

Description

The c.1942C>T variant is not present in publicly available database like Exome Variant Server (EVS), however present in 1000 Genomes, Exome Aggregation Consortium (ExAC), Genome Aggregation Database (gnomAD) and dbSNP at a low minor allele frequency (MAF<0.001), including one homozygote. The variant is present in our in-house exome database in heterozygous state (MAF~0.005). The variant was reported to ClinVar (Accession ID: VCV000351908.2) with conflicting interpretation of pathogenicity (likely benign/uncertain significance). In-silico pathogenicity prediction programslike SIFT, PolyPhen-2, MutationTaster2, CADD etc. predicted this variant as likely deleterious, however functional assay was not done to prove this. Due to lack of enough evidence the variant has been classified as uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Sep 16, 2024