NM_014363.6(SACS):c.9119dup (p.Asn3040fs) AND Spastic paraplegia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 13, 2023
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:: RCV001885404.4

Allele description [Variation Report for NM_014363.6(SACS):c.9119dup (p.Asn3040fs)]

NM_014363.6(SACS):c.9119dup (p.Asn3040fs)

Gene:

SACS:sacsin molecular chaperone [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

13q12.12

Genomic location:

Preferred name:

NM_014363.6(SACS):c.9119dup (p.Asn3040fs)

HGVS:

NC_000013.11:g.23334761dup
NG_012342.1:g.103946dup
NM_001278055.2:c.8678dup
NM_014363.6:c.9119dupMANE SELECT
NP_001264984.1:p.Asn2893fs
NP_055178.3:p.Asn3040fs
NC_000013.10:g.23908895_23908896insT
NC_000013.10:g.23908900dup
NM_014363.5:c.9119_9120insA

Protein change:

N2893fs

Links:

dbSNP: rs1435126137

NCBI 1000 Genomes Browser:

rs1435126137

Molecular consequence:

NM_001278055.2:c.8678dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_014363.6:c.9119dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Spastic paraplegia
Identifiers:: MedGen: C0037772; Human Phenotype Ontology: HP:0001258

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002151245	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 13, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 29449188, 15156359, 21507954, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002151245

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 13, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Novel homozygous variants in ATCAY, MCOLN1, and SACS in complex neurological disorders.

Manzoor H, Brüggemann N, Hussain HMJ, Bäumer T, Hinrichs F, Wajid M, Münchau A, Naz S, Lohmann K.

Parkinsonism Relat Disord. 2018 Jun;51:91-95. doi: 10.1016/j.parkreldis.2018.02.005. Epub 2018 Feb 6.

PubMed [citation]

PMID:: 29449188

Private SACS mutations in autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) families from Turkey.

Richter AM, Ozgul RK, Poisson VC, Topaloglu H.

Neurogenetics. 2004 Sep;5(3):165-70. Epub 2004 May 20.

PubMed [citation]

PMID:: 15156359

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002151245.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Asn3040Lysfs*5) in the SACS gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 1540 amino acid(s) of the SACS protein. This variant is present in population databases (no rsID available, gnomAD 0.01%). This premature translational stop signal has been observed in individual(s) with hereditary spastic paraplegia (PMID: 29449188). This variant is also known as c.9119dupA; p.Asn3040Lysfs*4. ClinVar contains an entry for this variant (Variation ID: 1344007). This variant disrupts a region of the SACS protein in which other variant(s) (p.Asn4549Asp) have been determined to be pathogenic (PMID: 15156359, 21507954). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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