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NM_001244008.2(KIF1A):c.37C>T (p.Arg13Cys) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 27, 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:
RCV001057550.8

Allele description [Variation Report for NM_001244008.2(KIF1A):c.37C>T (p.Arg13Cys)]

NM_001244008.2(KIF1A):c.37C>T (p.Arg13Cys)

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.37C>T (p.Arg13Cys)
HGVS:
  • NC_000002.12:g.240797716G>A
  • NG_029724.1:g.27492C>T
  • NM_001244008.2:c.37C>TMANE SELECT
  • NM_001320705.2:c.37C>T
  • NM_001330289.2:c.37C>T
  • NM_001330290.2:c.37C>T
  • NM_001379631.1:c.37C>T
  • NM_001379632.1:c.37C>T
  • NM_001379633.1:c.37C>T
  • NM_001379634.1:c.37C>T
  • NM_001379635.1:c.37C>T
  • NM_001379636.1:c.37C>T
  • NM_001379637.1:c.37C>T
  • NM_001379638.1:c.37C>T
  • NM_001379639.1:c.37C>T
  • NM_001379640.1:c.37C>T
  • NM_001379641.1:c.37C>T
  • NM_001379642.1:c.37C>T
  • NM_001379645.1:c.37C>T
  • NM_001379646.1:c.37C>T
  • NM_001379648.1:c.37C>T
  • NM_001379649.1:c.37C>T
  • NM_001379650.1:c.37C>T
  • NM_001379651.1:c.37C>T
  • NM_001379653.1:c.37C>T
  • NM_004321.8:c.37C>T
  • NP_001230937.1:p.Arg13Cys
  • NP_001307634.1:p.Arg13Cys
  • NP_001317218.1:p.Arg13Cys
  • NP_001317219.1:p.Arg13Cys
  • NP_001366560.1:p.Arg13Cys
  • NP_001366561.1:p.Arg13Cys
  • NP_001366562.1:p.Arg13Cys
  • NP_001366563.1:p.Arg13Cys
  • NP_001366564.1:p.Arg13Cys
  • NP_001366565.1:p.Arg13Cys
  • NP_001366566.1:p.Arg13Cys
  • NP_001366567.1:p.Arg13Cys
  • NP_001366568.1:p.Arg13Cys
  • NP_001366569.1:p.Arg13Cys
  • NP_001366570.1:p.Arg13Cys
  • NP_001366571.1:p.Arg13Cys
  • NP_001366574.1:p.Arg13Cys
  • NP_001366575.1:p.Arg13Cys
  • NP_001366577.1:p.Arg13Cys
  • NP_001366578.1:p.Arg13Cys
  • NP_001366579.1:p.Arg13Cys
  • NP_001366580.1:p.Arg13Cys
  • NP_001366582.1:p.Arg13Cys
  • NP_004312.2:p.Arg13Cys
  • LRG_367:g.27492C>T
  • NC_000002.11:g.241737133G>A
  • NM_004321.6:c.37C>T
Protein change:
R13C
Links:
dbSNP: rs1064794935
NCBI 1000 Genomes Browser:
rs1064794935
Molecular consequence:
  • NM_001244008.2:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001320705.2:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330289.2:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330290.2:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379631.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379632.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379633.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379634.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379635.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379636.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379637.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379638.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379639.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379640.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379641.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379642.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379645.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379646.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379648.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379649.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379650.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379651.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379653.1:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004321.8:c.37C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary spastic paraplegia 30
Synonyms:
Spastic paraplegia 30, autosomal recessive; SPASTIC PARAPLEGIA 30, AUTOSOMAL DOMINANT
Identifiers:
MONDO: MONDO:0012476; MedGen: C5235139; Orphanet: 101010; OMIM: 610357
Name:
Neuropathy, hereditary sensory, type 2C
Synonyms:
Hereditary sensory and autonomic neuropathy type IIC
Identifiers:
MONDO: MONDO:0013634; MedGen: C3280168; Orphanet: 970; OMIM: 614213
Name:
Intellectual disability, autosomal dominant 9 (NESCAVS)
Synonyms:
Mental retardation, autosomal dominant 9; NESCAV SYNDROME
Identifiers:
MONDO: MONDO:0013656; MedGen: C5393830; OMIM: 614255

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001222048Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 27, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

A Novel de novo KIF1A Mutation in a Patient with Autism, Hyperactivity, Epilepsy, Sensory Disturbance, and Spastic Paraplegia.

Kurihara M, Ishiura H, Bannai T, Mitsui J, Yoshimura J, Morishita S, Hayashi T, Shimizu J, Toda T, Tsuji S.

Intern Med. 2020 Mar 15;59(6):839-842. doi: 10.2169/internalmedicine.3661-19. Epub 2019 Dec 6.

PubMed [citation]
PMID:
31813911
PMCID:
PMC7118386

A de novo dominant mutation in KIF1A associated with axonal neuropathy, spasticity and autism spectrum disorder.

Tomaselli PJ, Rossor AM, Horga A, Laura M, Blake JC, Houlden H, Reilly MM.

J Peripher Nerv Syst. 2017 Dec;22(4):460-463. doi: 10.1111/jns.12235. Epub 2017 Sep 11.

PubMed [citation]
PMID:
28834584
PMCID:
PMC5763335
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001222048.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 13 of the KIF1A protein (p.Arg13Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with autosomal dominant hereditary spastic paraplegia (PMID: 31813911; Invitae). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 426934). 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 expected to disrupt KIF1A protein function with a positive predictive value of 95%. This variant disrupts the p.Arg13 amino acid residue in KIF1A. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 28834584). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: May 12, 2024