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NM_001244008.2(KIF1A):c.206C>T (p.Ser69Leu) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 20, 2022
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:
RCV000693147.11

Allele description [Variation Report for NM_001244008.2(KIF1A):c.206C>T (p.Ser69Leu)]

NM_001244008.2(KIF1A):c.206C>T (p.Ser69Leu)

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.206C>T (p.Ser69Leu)
HGVS:
  • NC_000002.12:g.240788208G>A
  • NG_029724.1:g.37000C>T
  • NM_001244008.2:c.206C>TMANE SELECT
  • NM_001320705.2:c.206C>T
  • NM_001330289.2:c.206C>T
  • NM_001330290.2:c.206C>T
  • NM_001379631.1:c.206C>T
  • NM_001379632.1:c.206C>T
  • NM_001379633.1:c.206C>T
  • NM_001379634.1:c.206C>T
  • NM_001379635.1:c.206C>T
  • NM_001379636.1:c.206C>T
  • NM_001379637.1:c.206C>T
  • NM_001379638.1:c.206C>T
  • NM_001379639.1:c.206C>T
  • NM_001379640.1:c.206C>T
  • NM_001379641.1:c.206C>T
  • NM_001379642.1:c.206C>T
  • NM_001379645.1:c.206C>T
  • NM_001379646.1:c.206C>T
  • NM_001379648.1:c.206C>T
  • NM_001379649.1:c.206C>T
  • NM_001379650.1:c.206C>T
  • NM_001379651.1:c.206C>T
  • NM_001379653.1:c.206C>T
  • NM_004321.8:c.206C>T
  • NP_001230937.1:p.Ser69Leu
  • NP_001230937.1:p.Ser69Leu
  • NP_001307634.1:p.Ser69Leu
  • NP_001317218.1:p.Ser69Leu
  • NP_001317219.1:p.Ser69Leu
  • NP_001366560.1:p.Ser69Leu
  • NP_001366561.1:p.Ser69Leu
  • NP_001366562.1:p.Ser69Leu
  • NP_001366563.1:p.Ser69Leu
  • NP_001366564.1:p.Ser69Leu
  • NP_001366565.1:p.Ser69Leu
  • NP_001366566.1:p.Ser69Leu
  • NP_001366567.1:p.Ser69Leu
  • NP_001366568.1:p.Ser69Leu
  • NP_001366569.1:p.Ser69Leu
  • NP_001366570.1:p.Ser69Leu
  • NP_001366571.1:p.Ser69Leu
  • NP_001366574.1:p.Ser69Leu
  • NP_001366575.1:p.Ser69Leu
  • NP_001366577.1:p.Ser69Leu
  • NP_001366578.1:p.Ser69Leu
  • NP_001366579.1:p.Ser69Leu
  • NP_001366580.1:p.Ser69Leu
  • NP_001366582.1:p.Ser69Leu
  • NP_004312.2:p.Ser69Leu
  • NP_004312.2:p.Ser69Leu
  • LRG_367t1:c.206C>T
  • LRG_367t2:c.206C>T
  • LRG_367:g.37000C>T
  • LRG_367p1:p.Ser69Leu
  • LRG_367p2:p.Ser69Leu
  • NC_000002.11:g.241727625G>A
  • NM_001244008.1:c.206C>T
  • NM_004321.6:c.206C>T
  • NM_004321.7:c.206C>T
  • Q12756:p.Ser69Leu
Protein change:
S69L; SER69LEU
Links:
UniProtKB: Q12756#VAR_077467; OMIM: 601255.0014; dbSNP: rs786200949
NCBI 1000 Genomes Browser:
rs786200949
Molecular consequence:
  • NM_001244008.2:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001320705.2:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330289.2:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330290.2:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379631.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379632.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379633.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379634.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379635.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379636.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379637.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379638.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379639.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379640.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379641.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379642.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379645.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379646.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379648.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379649.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379650.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379651.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379653.1:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004321.8:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary spastic paraplegia 30
Synonyms:
Spastic paraplegia 30, autosomal recessive; SPASTIC PARAPLEGIA 30A, 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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000821003Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Dec 20, 2022)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Dominant transmission of de novo KIF1A motor domain variant underlying pure spastic paraplegia.

Ylikallio E, Kim D, Isohanni P, Auranen M, Kim E, Lönnqvist T, Tyynismaa H.

Eur J Hum Genet. 2015 Oct;23(10):1427-30. doi: 10.1038/ejhg.2014.297. Epub 2015 Jan 14.

PubMed [citation]
PMID:
25585697
PMCID:
PMC4592090

Variants in KIF1A gene in dominant and sporadic forms of hereditary spastic paraparesis.

Citterio A, Arnoldi A, Panzeri E, Merlini L, D'Angelo MG, Musumeci O, Toscano A, Bondi A, Martinuzzi A, Bresolin N, Bassi MT.

J Neurol. 2015 Dec;262(12):2684-90. doi: 10.1007/s00415-015-7899-9. Epub 2015 Sep 26.

PubMed [citation]
PMID:
26410750
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000821003.7

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

Description

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. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 188057). This missense change has been observed in individual(s) with uncomplicated hereditary spastic paraplegia (PMID: 25585697, 26410750). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 69 of the KIF1A protein (p.Ser69Leu).

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

Last Updated: Oct 20, 2024