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NM_001365951.3(KIF1B):c.3079C>T (p.Arg1027Ter) AND Charcot-Marie-Tooth disease type 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 11, 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:
RCV003743695.1

Allele description [Variation Report for NM_001365951.3(KIF1B):c.3079C>T (p.Arg1027Ter)]

NM_001365951.3(KIF1B):c.3079C>T (p.Arg1027Ter)

Gene:
KIF1B:kinesin family member 1B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.22
Genomic location:
Preferred name:
NM_001365951.3(KIF1B):c.3079C>T (p.Arg1027Ter)
HGVS:
  • NC_000001.11:g.10336692C>T
  • NG_008069.1:g.130987C>T
  • NM_001365951.3:c.3079C>TMANE SELECT
  • NM_001365952.1:c.3079C>T
  • NM_015074.3:c.2941C>T
  • NP_001352880.1:p.Arg1027Ter
  • NP_001352881.1:p.Arg1027Ter
  • NP_055889.2:p.Arg981Ter
  • LRG_252t1:c.2941C>T
  • LRG_252t2:c.3079C>T
  • LRG_252:g.130987C>T
  • LRG_252p1:p.Arg981Ter
  • LRG_252p2:p.Arg1027Ter
  • NC_000001.10:g.10396750C>T
Protein change:
R1027*
Links:
dbSNP: rs886042662
NCBI 1000 Genomes Browser:
rs886042662
Molecular consequence:
  • NM_001365951.3:c.3079C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001365952.1:c.3079C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_015074.3:c.2941C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Charcot-Marie-Tooth disease type 2
Synonyms:
Charcot-Marie-Tooth, Type 2
Identifiers:
MONDO: MONDO:0018993; MedGen: C0270914

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004559341Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jun 11, 2023)
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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV004559341.1

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

Description

This variant has not been reported in the literature in individuals affected with KIF1B-related conditions. 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 sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 283613). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg981*) in the KIF1B gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in KIF1B cause disease.

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

Last Updated: Jun 23, 2024