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NM_014946.4(SPAST):c.1164G>T (p.Lys388Asn) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 6, 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:
RCV000521931.1

Allele description [Variation Report for NM_014946.4(SPAST):c.1164G>T (p.Lys388Asn)]

NM_014946.4(SPAST):c.1164G>T (p.Lys388Asn)

Gene:
SPAST:spastin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p22.3
Genomic location:
Preferred name:
NM_014946.4(SPAST):c.1164G>T (p.Lys388Asn)
HGVS:
  • NC_000002.12:g.32127013G>T
  • NG_008730.1:g.68403G>T
  • NM_001363823.2:c.1161G>T
  • NM_001363875.2:c.1065G>T
  • NM_001377959.1:c.1068G>T
  • NM_014946.4:c.1164G>TMANE SELECT
  • NM_199436.2:c.1068G>T
  • NP_001350752.1:p.Lys387Asn
  • NP_001350804.1:p.Lys355Asn
  • NP_001364888.1:p.Lys356Asn
  • NP_055761.2:p.Lys388Asn
  • NP_055761.2:p.Lys388Asn
  • NP_955468.1:p.Lys356Asn
  • LRG_714t1:c.1164G>T
  • LRG_714:g.68403G>T
  • LRG_714p1:p.Lys388Asn
  • NC_000002.11:g.32352082G>T
  • NM_014946.3:c.1164G>T
Protein change:
K355N
Links:
dbSNP: rs1553316838
NCBI 1000 Genomes Browser:
rs1553316838
Molecular consequence:
  • NM_001363823.2:c.1161G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363875.2:c.1065G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377959.1:c.1068G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014946.4:c.1164G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_199436.2:c.1068G>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
SCV000618811GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Jul 6, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000618811.2

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

Description

The K388N variant in the SPAST gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The K388N variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The K388N variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a conserved position within the ATPase domain. Missense variants in nearby residues (G385W, G385E, N386S, N386K, M390V, M390I, L391Q, L391P) have been reported in the Human Gene Mutation Database in association with spastic paraplegia (Stenson et al., 2014), supporting the functional importance of this region of the protein. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret K388N as a pathogenic variant.

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

Last Updated: Sep 29, 2024