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NM_001244008.2(KIF1A):c.920G>A (p.Arg307Gln)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Sep 29, 2021)
Last evaluated:
Jun 16, 2020
Accession:
VCV000418275.5
Variation ID:
418275
Description:
single nucleotide variant
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NM_001244008.2(KIF1A):c.920G>A (p.Arg307Gln)

Allele ID
405684
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 240775889 (GRCh38) GRCh38 UCSC
2: 241715306 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001244008.1:c.920G>A NP_001230937.1:p.Arg307Gln missense
NM_004321.7:c.920G>A NP_004312.2:p.Arg307Gln missense
NC_000002.11:g.241715306C>T
... more HGVS
Protein change
R307Q
Other names
-
Canonical SPDI
NC_000002.12:240775888:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA16617510
dbSNP: rs1064793161
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 Jun 15, 2020 RCV000496175.3
Pathogenic 1 criteria provided, single submitter Jun 16, 2020 RCV000480291.3
Pathogenic 1 criteria provided, single submitter May 20, 2018 RCV000705000.1
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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
1335 1436

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jun 16, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000565098.4
Submitted: (Sep 29, 2021)
Evidence details
Comment:
Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; … (more)
Pathogenic
(Jan 06, 2017)
criteria provided, single submitter
Method: clinical testing
Mental retardation, autosomal dominant 9
Allele origin: de novo
Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement,Assistance Publique Hopitaux de Paris
Accession: SCV000586758.1
Submitted: (Aug 01, 2017)
Evidence details
Publications
PubMed (1)
Comment:
neurodegenerative syndrome; Intellectual disability; hypotonia; cerebellar atrophy; optic nerve atrophy; congenital retinal dystrophy; pyramidal syndrome (Rossolimo and Babinsky signs)
Pathogenic
(May 20, 2018)
criteria provided, single submitter
Method: clinical testing
Spastic paraplegia 30, autosomal recessive
Hereditary sensory and autonomic neuropathy type IIC
Mental retardation, autosomal dominant 9
Allele origin: germline
Invitae
Accession: SCV000833977.1
Submitted: (Aug 29, 2018)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change replaces arginine with glutamine at codon 307 of the KIF1A protein (p.Arg307Gln). The arginine residue is highly conserved and there is a … (more)
Likely pathogenic
(Dec 03, 2018)
criteria provided, single submitter
Method: research
Intellectual disability, autosomal dominant 9
(Autosomal dominant inheritance)
Allele origin: de novo
Broad Institute Rare Disease Group, Broad Institute
Accession: SCV001164442.1
Submitted: (Oct 03, 2019)
Evidence details
Comment:
The heterozyous p.Arg307Gln variant in KIF1A was identified by our study in one individual with GLUT1 deficiency syndrome. Trio exome analysis showed this variant to … (more)
Likely pathogenic
(Jun 15, 2020)
criteria provided, single submitter
Method: curation
Intellectual disability, autosomal dominant 9
Allele origin: unknown
SIB Swiss Institute of Bioinformatics
Accession: SCV001426722.1
Submitted: (Jun 17, 2020)
Evidence details
Publications
PubMed (2)
Comment:
This variant is interpreted as likely pathogenic for NESCAV syndrome, autosomal dominant. The following ACMG Tag(s) were applied: Absent from controls (or at extremely low … (more)

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
Using medical exome sequencing to identify the causes of neurodevelopmental disorders: Experience of 2 clinical units and 216 patients. Chérot E Clinical genetics 2018 PMID: 28708303
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Novel De Novo Mutations in KIF1A as a Cause of Hereditary Spastic Paraplegia With Progressive Central Nervous System Involvement. Hotchkiss L Journal of child neurology 2016 PMID: 27034427
De novo KIF1A mutations cause intellectual deficit, cerebellar atrophy, lower limb spasticity and visual disturbance. Ohba C Journal of human genetics 2015 PMID: 26354034

Text-mined citations for rs1064793161...

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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 Nov 27, 2021