NM_014363.6(SACS):c.382_383del (p.Glu128fs) AND Spastic paraplegia

Clinical significance:Pathogenic (Last evaluated: Feb 22, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001062044.1

Allele description [Variation Report for NM_014363.6(SACS):c.382_383del (p.Glu128fs)]

NM_014363.6(SACS):c.382_383del (p.Glu128fs)

Gene:
SACS:sacsin molecular chaperone [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
13q12.12
Genomic location:
Preferred name:
NM_014363.6(SACS):c.382_383del (p.Glu128fs)
HGVS:
  • NC_000013.11:g.23365241_23365242del
  • NG_012342.1:g.73462_73463del
  • NM_001278055.2:c.-60_-59del
  • NM_014363.6:c.382_383delMANE SELECT
  • NP_055178.3:p.Glu128fs
  • NC_000013.10:g.23939380_23939381del
  • NM_014363.4:c.382_383del
  • NM_014363.5:c.382_383del
Protein change:
E128fs
Molecular consequence:
  • NM_001278055.2:c.-60_-59del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_014363.6:c.382_383del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Spastic paraplegia
Synonyms:
Spastic paraplegia, lower limb
Identifiers:
MedGen: C0037772; Human Phenotype Ontology: HP:0001258

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001226814Invitaecriteria provided, single submitter
Pathogenic
(Feb 22, 2019)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001226814.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change creates a premature translational stop signal (p.Glu128Serfs*2) in the SACS gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs757179309, ExAC 0.01%). This variant has not been reported in the literature in individuals with SACS-related conditions. Loss-of-function variants in SACS are known to be pathogenic (PMID: 18465152, 20876471). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Jan 30, 2021

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