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

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Jul 20, 2021)
Last evaluated:
Apr 15, 2021
Accession:
VCV000245636.10
Variation ID:
245636
Description:
single nucleotide variant
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NM_001244008.2(KIF1A):c.760C>T (p.Arg254Trp)

Allele ID
244362
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 240783777 (GRCh38) GRCh38 UCSC
2: 241723194 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_367:g.41431C>T
LRG_367t1:c.760C>T LRG_367p1:p.Arg254Trp
NC_000002.11:g.241723194G>A
... more HGVS
Protein change
R254W
Other names
-
Canonical SPDI
NC_000002.12:240783776:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA10584198
OMIM: 601255.0012
dbSNP: rs879253888
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Apr 15, 2021 RCV000236491.6
Pathogenic 3 criteria provided, multiple submitters, no conflicts Jun 15, 2020 RCV000995795.4
Pathogenic 1 criteria provided, single submitter Feb 19, 2016 RCV000623278.1
Likely pathogenic 1 criteria provided, single submitter Oct 31, 2018 RCV000763486.1

Clinical features observed in individuals with this variant

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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KIF1A No evidence available No evidence available GRCh38
GRCh37
1302 1403

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jun 08, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000700740.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary sensory and autonomic neuropathy type IIA
Spastic paraplegia 30, autosomal recessive
Hereditary sensory and autonomic neuropathy type IIC
Intellectual disability, autosomal dominant 9
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000894271.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Pathogenic
(Jan 30, 2018)
criteria provided, single submitter
Method: clinical testing
Intellectual disability, autosomal dominant 9
(Autosomal dominant inheritance)
Allele origin: de novo
Institute of Human Genetics, Klinikum rechts der Isar
Accession: SCV001150146.1
Submitted: (Jan 21, 2020)
Evidence details
Pathogenic
(Jun 15, 2020)
criteria provided, single submitter
Method: curation
Intellectual disability, autosomal dominant 9
Allele origin: unknown
SIB Swiss Institute of Bioinformatics
Accession: SCV001426707.1
Submitted: (Jun 17, 2020)
Evidence details
Publications
PubMed (2)
Comment:
This variant is interpreted as pathogenic for NESCAV syndrome, autosomal dominant. The following ACMG Tag(s) were applied: Absent from controls (or at extremely low frequency … (more)
Pathogenic
(Feb 19, 2016)
criteria provided, single submitter
Method: clinical testing
Inborn genetic diseases
Allele origin: germline
Ambry Genetics
Accession: SCV000741095.2
Submitted: (Oct 09, 2020)
Evidence details
Likely pathogenic
(Oct 23, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
(Unknown mechanism)
Allele origin: germline
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001446534.1
Submitted: (Oct 23, 2020)
Evidence details
Pathogenic
(Apr 15, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000292595.11
Submitted: (Jul 20, 2021)
Evidence details
Comment:
Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This … (more)
Pathogenic
(Apr 16, 2020)
no assertion criteria provided
Method: literature only
NESCAV SYNDROME
Allele origin: germline
OMIM
Accession: SCV001244201.1
Submitted: (Apr 16, 2020)
Evidence details
Publications
PubMed (1)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
KIF1A-related disorders in children: A wide spectrum of central and peripheral nervous system involvement. Nemani T Journal of the peripheral nervous system : JPNS 2020 PMID: 32096284
De novo KIF1A mutations cause intellectual deficit, cerebellar atrophy, lower limb spasticity and visual disturbance. Ohba C Journal of human genetics 2015 PMID: 26354034
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=KIF1A - - - -

Text-mined citations for rs879253888...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 16, 2021