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NM_001244008.2(KIF1A):c.2066C>T (p.Ser689Phe) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 1, 2017
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:
RCV000520574.1

Allele description [Variation Report for NM_001244008.2(KIF1A):c.2066C>T (p.Ser689Phe)]

NM_001244008.2(KIF1A):c.2066C>T (p.Ser689Phe)

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.2066C>T (p.Ser689Phe)
HGVS:
  • NC_000002.12:g.240762769G>A
  • NG_029724.1:g.62439C>T
  • NM_001244008.2:c.2066C>TMANE SELECT
  • NM_001320705.2:c.2066C>T
  • NM_001330289.2:c.2066C>T
  • NM_001330290.2:c.2141C>T
  • NM_001379631.1:c.2141C>T
  • NM_001379632.1:c.2039C>T
  • NM_001379633.1:c.2039C>T
  • NM_001379634.1:c.2141C>T
  • NM_001379635.1:c.2141C>T
  • NM_001379636.1:c.2039C>T
  • NM_001379637.1:c.2114C>T
  • NM_001379638.1:c.2066C>T
  • NM_001379639.1:c.2039C>T
  • NM_001379640.1:c.2039C>T
  • NM_001379641.1:c.2039C>T
  • NM_001379642.1:c.2039C>T
  • NM_001379645.1:c.2039C>T
  • NM_001379646.1:c.2141C>T
  • NM_001379648.1:c.2114C>T
  • NM_001379649.1:c.2039C>T
  • NM_001379650.1:c.2039C>T
  • NM_001379651.1:c.2039C>T
  • NM_001379653.1:c.2039C>T
  • NM_004321.8:c.2039C>T
  • NP_001230937.1:p.Ser689Phe
  • NP_001307634.1:p.Ser689Phe
  • NP_001317218.1:p.Ser689Phe
  • NP_001317219.1:p.Ser714Phe
  • NP_001366560.1:p.Ser714Phe
  • NP_001366561.1:p.Ser680Phe
  • NP_001366562.1:p.Ser680Phe
  • NP_001366563.1:p.Ser714Phe
  • NP_001366564.1:p.Ser714Phe
  • NP_001366565.1:p.Ser680Phe
  • NP_001366566.1:p.Ser705Phe
  • NP_001366567.1:p.Ser689Phe
  • NP_001366568.1:p.Ser680Phe
  • NP_001366569.1:p.Ser680Phe
  • NP_001366570.1:p.Ser680Phe
  • NP_001366571.1:p.Ser680Phe
  • NP_001366574.1:p.Ser680Phe
  • NP_001366575.1:p.Ser714Phe
  • NP_001366577.1:p.Ser705Phe
  • NP_001366578.1:p.Ser680Phe
  • NP_001366579.1:p.Ser680Phe
  • NP_001366580.1:p.Ser680Phe
  • NP_001366582.1:p.Ser680Phe
  • NP_004312.2:p.Ser680Phe
  • LRG_367:g.62439C>T
  • NC_000002.11:g.241702186G>A
  • NM_004321.6:c.2039C>T
Protein change:
S680F
Links:
dbSNP: rs1553633725
NCBI 1000 Genomes Browser:
rs1553633725
Molecular consequence:
  • NM_001244008.2:c.2066C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001320705.2:c.2066C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330289.2:c.2066C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330290.2:c.2141C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379631.1:c.2141C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379632.1:c.2039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379633.1:c.2039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379634.1:c.2141C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379635.1:c.2141C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379636.1:c.2039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379637.1:c.2114C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379638.1:c.2066C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379639.1:c.2039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379640.1:c.2039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379641.1:c.2039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379642.1:c.2039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379645.1:c.2039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379646.1:c.2141C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379648.1:c.2114C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379649.1:c.2039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379650.1:c.2039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379651.1:c.2039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001379653.1:c.2039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004321.8:c.2039C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000619772GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Aug 1, 2017) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000619772.1

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

Description

A variant of uncertain significance has been identified in the KIF1A gene. The S680F variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The S680F variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The S680F variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. However, this amino acid substitution does not occur within the predicted motor domain of the protein, where all pathogenic missense KIF1A pathogenic variants have been identified to-date (Lee et al., 2014). Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: Feb 28, 2024