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NM_014946.4(SPAST):c.1495C>T (p.Arg499Cys) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Jan 13, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000523541.19

Allele description [Variation Report for NM_014946.4(SPAST):c.1495C>T (p.Arg499Cys)]

NM_014946.4(SPAST):c.1495C>T (p.Arg499Cys)

Gene:
SPAST:spastin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p22.3
Genomic location:
Preferred name:
NM_014946.4(SPAST):c.1495C>T (p.Arg499Cys)
HGVS:
  • NC_000002.12:g.32141905C>T
  • NG_008730.1:g.83295C>T
  • NM_001363823.2:c.1492C>T
  • NM_001363875.2:c.1396C>T
  • NM_001377959.1:c.1399C>T
  • NM_014946.4:c.1495C>TMANE SELECT
  • NM_199436.2:c.1399C>T
  • NP_001350752.1:p.Arg498Cys
  • NP_001350804.1:p.Arg466Cys
  • NP_001364888.1:p.Arg467Cys
  • NP_055761.2:p.Arg499Cys
  • NP_055761.2:p.Arg499Cys
  • NP_955468.1:p.Arg467Cys
  • LRG_714t1:c.1495C>T
  • LRG_714:g.83295C>T
  • LRG_714p1:p.Arg499Cys
  • NC_000002.11:g.32366974C>T
  • NM_014946.3:c.1495C>T
  • Q9UBP0:p.Arg499Cys
Protein change:
R466C; ARG499CYS
Links:
UniProtKB: Q9UBP0#VAR_010198; OMIM: 604277.0004; dbSNP: rs121908511
NCBI 1000 Genomes Browser:
rs121908511
Molecular consequence:
  • NM_001363823.2:c.1492C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363875.2:c.1396C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377959.1:c.1399C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014946.4:c.1495C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_199436.2:c.1399C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000617691GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Jan 13, 2022)
germlineclinical testing

Citation Link,

SCV001247360CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Pathogenic
(Sep 1, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000617691.4

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

Description

Published functional studies demonstrate a damaging effect on microtubule disassembly and ATPase activity (Errico et al., 2002; Evans et al., 2005); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29980238, 31751864, 15716377, 29934652, 30780198, 30476002, 31285604, 28191889, 34950521, Varghaei2021[pdf], 21139634, 26094131, 17957230, 18701882, 11809724, 11309678, 10610178)

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

From CeGaT Center for Human Genetics Tuebingen, SCV001247360.22

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 17, 2024