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NM_014946.4(SPAST):c.419G>A (p.Gly140Glu) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 15, 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:
RCV002282706.1

Allele description [Variation Report for NM_014946.4(SPAST):c.419G>A (p.Gly140Glu)]

NM_014946.4(SPAST):c.419G>A (p.Gly140Glu)

Gene:
SPAST:spastin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p22.3
Genomic location:
Preferred name:
NM_014946.4(SPAST):c.419G>A (p.Gly140Glu)
HGVS:
  • NC_000002.12:g.32087495G>A
  • NG_008730.1:g.28885G>A
  • NM_001363823.2:c.416G>A
  • NM_001363875.2:c.416G>A
  • NM_001377959.1:c.419G>A
  • NM_014946.4:c.419G>AMANE SELECT
  • NM_199436.2:c.419G>A
  • NP_001350752.1:p.Gly139Glu
  • NP_001350804.1:p.Gly139Glu
  • NP_001364888.1:p.Gly140Glu
  • NP_055761.2:p.Gly140Glu
  • NP_955468.1:p.Gly140Glu
  • LRG_714t1:c.419G>A
  • LRG_714:g.28885G>A
  • NC_000002.11:g.32312564G>A
  • NM_014946.3:c.419G>A
Protein change:
G139E
Links:
dbSNP: rs763649847
NCBI 1000 Genomes Browser:
rs763649847
Molecular consequence:
  • NM_001363823.2:c.416G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363875.2:c.416G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377959.1:c.419G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014946.4:c.419G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_199436.2:c.419G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002572054Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Aug 15, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002572054.1

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

Description

Variant summary: SPAST c.419G>A (p.Gly140Glu) results in a non-conservative amino acid change located in the MIT domain (IPR007330) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 250968 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.419G>A in individuals affected with Spastic Paraplegia and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted a clinical-significance assessment for this variant to ClinVar after 2014 and classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Dec 24, 2023