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NM_014363.6(SACS):c.8956C>G (p.His2986Asp) AND Spastic paraplegia

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 12, 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:
RCV002531348.2

Allele description [Variation Report for NM_014363.6(SACS):c.8956C>G (p.His2986Asp)]

NM_014363.6(SACS):c.8956C>G (p.His2986Asp)

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.8956C>G (p.His2986Asp)
HGVS:
  • NC_000013.11:g.23334920G>C
  • NG_012342.1:g.103783C>G
  • NM_001278055.2:c.8515C>G
  • NM_014363.6:c.8956C>GMANE SELECT
  • NP_001264984.1:p.His2839Asp
  • NP_055178.3:p.His2986Asp
  • NC_000013.10:g.23909059G>C
  • NM_014363.4:c.8956C>G
Protein change:
H2839D
Links:
dbSNP: rs751888795
NCBI 1000 Genomes Browser:
rs751888795
Molecular consequence:
  • NM_001278055.2:c.8515C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014363.6:c.8956C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003289416Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 12, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

A multicenter clinical exome study in unselected cohorts from a consanguineous population of Saudi Arabia demonstrated a high diagnostic yield.

Alfares A, Alfadhel M, Wani T, Alsahli S, Alluhaydan I, Al Mutairi F, Alothaim A, Albalwi M, Al Subaie L, Alturki S, Al-Twaijri W, Alrifai M, Al-Rumayya A, Alameer S, Faqeeh E, Alasmari A, Alsamman A, Tashkandia S, Alghamdi A, Alhashem A, Tabarki B, AlShahwan S, et al.

Mol Genet Metab. 2017 Jun;121(2):91-95. doi: 10.1016/j.ymgme.2017.04.002. Epub 2017 Apr 7. No abstract available.

PubMed [citation]
PMID:
28454995

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003289416.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change replaces histidine, which is basic and polar, with aspartic acid, which is acidic and polar, at codon 2986 of the SACS protein (p.His2986Asp). This variant is present in population databases (rs751888795, gnomAD 0.003%). This missense change has been observed in individual(s) with spastic ataxia (PMID: 28454995). ClinVar contains an entry for this variant (Variation ID: 558044). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SACS protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024