NM_014363.6(SACS):c.3427C>T (p.Gln1143Ter) AND Charlevoix-Saguenay spastic ataxia

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Sep 5, 2021
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:: RCV000670813.4

Allele description [Variation Report for NM_014363.6(SACS):c.3427C>T (p.Gln1143Ter)]

NM_014363.6(SACS):c.3427C>T (p.Gln1143Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

13q12.12

Genomic location:

Preferred name:

NM_014363.6(SACS):c.3427C>T (p.Gln1143Ter)

HGVS:

NC_000013.11:g.23340449G>A
NG_012342.1:g.98254C>T
NM_001278055.2:c.2986C>T
NM_014363.6:c.3427C>TMANE SELECT
NP_001264984.1:p.Gln996Ter
NP_055178.3:p.Gln1143Ter
NC_000013.10:g.23914588G>A
NM_014363.4:c.3427C>T

Protein change:

Q1143*

Links:

dbSNP: rs144267558

NCBI 1000 Genomes Browser:

rs144267558

Molecular consequence:

NM_001278055.2:c.2986C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_014363.6:c.3427C>T - nonsense - [Sequence Ontology: SO:0001587]

Functional consequence:

No function

Observations:

Condition(s)

Name:: Charlevoix-Saguenay spastic ataxia (SACS)
Synonyms:: Autosomal recessive spastic ataxia of Charlevoix-Saguenay; Spastic ataxia of Charlevoix-Saguenay; SPASTIC ATAXIA 6, AUTOSOMAL RECESSIVE
Identifiers:: MONDO: MONDO:0010041; MedGen: C1849140; Orphanet: 98; OMIM: 270550

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000795713	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely pathogenic (Nov 13, 2017)	unknown	clinical testing	Citation Link,
SCV001622771	Medical Genetics Laboratory, Tarbiat Modares University	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 1, 2020)	inherited	clinical testing	PubMed (2) [See all records that cite these PMIDs] 20876471, 25741868
SCV002027662	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Sep 5, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000795713

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Likely pathogenic
(Nov 13, 2017)

unknown

clinical testing

Citation Link,

SCV001622771

Medical Genetics Laboratory, Tarbiat Modares University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 1, 2020)

inherited

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV002027662

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Sep 5, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
Persian	inherited	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in SACS cause atypical and late-onset forms of ARSACS.

Baets J, Deconinck T, Smets K, Goossens D, Van den Bergh P, Dahan K, Schmedding E, Santens P, Rasic VM, Van Damme P, Robberecht W, De Meirleir L, Michielsens B, Del-Favero J, Jordanova A, De Jonghe P.

Neurology. 2010 Sep 28;75(13):1181-8. doi: 10.1212/WNL.0b013e3181f4d86c.

PubMed [citation]

PMID:: 20876471

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Counsyl, SCV000795713.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

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

From Medical Genetics Laboratory, Tarbiat Modares University, SCV001622771.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Persian	1	not provided	not provided	clinical testing	PubMed (2)

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

From Genome-Nilou Lab, SCV002027662.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 23, 2022

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