NM_001365951.3(KIF1B):c.2846C>T (p.Thr949Met) AND Charcot-Marie-Tooth disease, type 2

Clinical significance:Uncertain significance (Last evaluated: Dec 5, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_001365951.3(KIF1B):c.2846C>T (p.Thr949Met)]

NM_001365951.3(KIF1B):c.2846C>T (p.Thr949Met)

KIF1B:kinesin family member 1B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001365951.3(KIF1B):c.2846C>T (p.Thr949Met)
  • NC_000001.11:g.10326281C>T
  • NG_008069.1:g.120576C>T
  • NM_001365951.3:c.2846C>TMANE SELECT
  • NM_001365952.1:c.2846C>T
  • NM_015074.3:c.2708C>T
  • NP_001352880.1:p.Thr949Met
  • NP_001352881.1:p.Thr949Met
  • NP_055889.2:p.Thr903Met
  • LRG_252t1:c.2708C>T
  • LRG_252t2:c.2846C>T
  • LRG_252:g.120576C>T
  • LRG_252p1:p.Thr903Met
  • LRG_252p2:p.Thr949Met
  • NC_000001.10:g.10386339C>T
Protein change:
Molecular consequence:
  • NM_001365951.3:c.2846C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365952.1:c.2846C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015074.3:c.2708C>T - missense variant - [Sequence Ontology: SO:0001583]


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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001212564Invitaecriteria provided, single submitter
Uncertain significance
(Dec 5, 2019)
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



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]

Details of each submission

From Invitae, SCV001212564.2

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


This sequence change replaces threonine with methionine at codon 903 of the KIF1B protein (p.Thr903Met). The threonine residue is moderately conserved and there is a moderate physicochemical difference between threonine and methionine. This variant is present in population databases (rs141942131, ExAC 0.01%). This variant has not been reported in the literature in individuals with KIF1B-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: Tolerated; PolyPhen-2: Possibly Damaging; Align-GVGD: Class C0. The methionine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.

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

Last Updated: Nov 20, 2021

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