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NM_001244008.2(KIF1A):c.760C>T (p.Arg254Trp) AND KIF1A-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 9, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV004737388.1

Allele description [Variation Report for NM_001244008.2(KIF1A):c.760C>T (p.Arg254Trp)]

NM_001244008.2(KIF1A):c.760C>T (p.Arg254Trp)

Gene:
KIF1A:kinesin family member 1A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q37.3
Genomic location:
Preferred name:
NM_001244008.2(KIF1A):c.760C>T (p.Arg254Trp)
HGVS:
  • NC_000002.12:g.240783777G>A
  • NG_029724.1:g.41431C>T
  • NM_001244008.2:c.760C>TMANE SELECT
  • NM_001320705.2:c.760C>T
  • NM_001330289.2:c.760C>T
  • NM_001330290.2:c.760C>T
  • NM_001379631.1:c.760C>T
  • NM_001379632.1:c.760C>T
  • NM_001379633.1:c.760C>T
  • NM_001379634.1:c.760C>T
  • NM_001379635.1:c.760C>T
  • NM_001379636.1:c.760C>T
  • NM_001379637.1:c.760C>T
  • NM_001379638.1:c.760C>T
  • NM_001379639.1:c.760C>T
  • NM_001379640.1:c.760C>T
  • NM_001379641.1:c.760C>T
  • NM_001379642.1:c.760C>T
  • NM_001379645.1:c.760C>T
  • NM_001379646.1:c.760C>T
  • NM_001379648.1:c.760C>T
  • NM_001379649.1:c.760C>T
  • NM_001379650.1:c.760C>T
  • NM_001379651.1:c.760C>T
  • NM_001379653.1:c.760C>T
  • NM_004321.8:c.760C>T
  • NP_001230937.1:p.Arg254Trp
  • NP_001230937.1:p.Arg254Trp
  • NP_001307634.1:p.Arg254Trp
  • NP_001317218.1:p.Arg254Trp
  • NP_001317219.1:p.Arg254Trp
  • NP_001366560.1:p.Arg254Trp
  • NP_001366561.1:p.Arg254Trp
  • NP_001366562.1:p.Arg254Trp
  • NP_001366563.1:p.Arg254Trp
  • NP_001366564.1:p.Arg254Trp
  • NP_001366565.1:p.Arg254Trp
  • NP_001366566.1:p.Arg254Trp
  • NP_001366567.1:p.Arg254Trp
  • NP_001366568.1:p.Arg254Trp
  • NP_001366569.1:p.Arg254Trp
  • NP_001366570.1:p.Arg254Trp
  • NP_001366571.1:p.Arg254Trp
  • NP_001366574.1:p.Arg254Trp
  • NP_001366575.1:p.Arg254Trp
  • NP_001366577.1:p.Arg254Trp
  • NP_001366578.1:p.Arg254Trp
  • NP_001366579.1:p.Arg254Trp
  • NP_001366580.1:p.Arg254Trp
  • NP_001366582.1:p.Arg254Trp
  • NP_004312.2:p.Arg254Trp
  • NP_004312.2:p.Arg254Trp
  • LRG_367t1:c.760C>T
  • LRG_367t2:c.760C>T
  • LRG_367:g.41431C>T
  • LRG_367p1:p.Arg254Trp
  • LRG_367p2:p.Arg254Trp
  • NC_000002.11:g.241723194G>A
  • NM_001244008.1:c.760C>T
  • NM_004321.5:c.760C>T
  • NM_004321.6:c.760C>T
  • NM_004321.7:c.760C>T
  • NM_001224008.1:c.760C>T
Protein change:
R254W; ARG254TRP
Links:
OMIM: 601255.0012; dbSNP: rs879253888
NCBI 1000 Genomes Browser:
rs879253888
Molecular consequence:
  • NM_001244008.2:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001320705.2:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330289.2:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330290.2:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379631.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379632.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379633.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379634.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379635.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379636.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379637.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379638.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379639.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379640.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379641.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379642.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379645.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379646.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379648.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379649.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379650.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379651.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379653.1:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004321.8:c.760C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
KIF1A-related disorder
Synonyms:
KIF1A-related disorders; KIF1A-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005346643PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Aug 9, 2024) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV005346643.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The KIF1A c.760C>T variant is predicted to result in the amino acid substitution p.Arg254Trp. This variant has been reported as a de novo finding in multiple individuals with autosomal dominant neurodegeneration and spasticity with or without cerebellar atrophy or cortical visual impairment (NESCAV) syndrome (Ohba et al. 2015. PubMed ID: 26354034; Sakamoto et al. 2022. PubMed ID: 36305856; Kim et al. 2023. PubMed ID: 37180992). This variant has not been reported in a large population database, indicating it is rare. An in vitro experimental study suggests this variant affects the KIF1A motor function (Boyle et al. 2021. PubMed ID: 33880452). An alternate missense change affecting the same amino acid (p.Arg254Gln) has been reported de novo in an individual with NESCAV syndrome (Ohba et al. 2015. PubMed ID: 26354034). In summary, the c.760C>T (p.Arg254Trp) variant is interpreted as pathogenic.

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

Last Updated: Oct 20, 2024