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NC_000013.10:g.(?_23667335)_(23985398_?)dup AND Spastic paraplegia

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 10, 2018
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:
RCV000537039.2

Allele description [Variation Report for NC_000013.10:g.(?_23667335)_(23985398_?)dup]

NC_000013.10:g.(?_23667335)_(23985398_?)dup

Genes:
  • LOC130009362:ATAC-STARR-seq lymphoblastoid active region 7449 [Gene]
  • LOC130009363:ATAC-STARR-seq lymphoblastoid active region 7450 [Gene]
  • LOC130009364:ATAC-STARR-seq lymphoblastoid active region 7451 [Gene]
  • LOC130009367:ATAC-STARR-seq lymphoblastoid active region 7452 [Gene]
  • LOC130009368:ATAC-STARR-seq lymphoblastoid active region 7453 [Gene]
  • LOC130009369:ATAC-STARR-seq lymphoblastoid active region 7454 [Gene]
  • LOC130009365:ATAC-STARR-seq lymphoblastoid silent region 5171 [Gene]
  • LOC130009366:ATAC-STARR-seq lymphoblastoid silent region 5172 [Gene]
  • LOC132090179:Neanderthal introgressed variant-containing enhancer experimental_32684 [Gene]
  • LINC00362:long intergenic non-protein coding RNA 362 [Gene - HGNC]
  • SACS:sacsin molecular chaperone [Gene - OMIM - HGNC]
  • SGCG:sarcoglycan gamma [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
13q12.12
Genomic location:
Preferred name:
NC_000013.10:g.(?_23667335)_(23985398_?)dup
HGVS:
NC_000013.10:g.(?_23667335)_(23985398_?)dup

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
SCV000634378Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 10, 2018) 		germlineclinical testing

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

Help

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

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000634378.2

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

Description

This variant results in a copy number gain of the genomic region encompassing the full coding sequence of the SACS gene. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. A copy number gain of only the SACS gene has not been reported in the literature in individuals with SACS-related disease. Experimental studies are not available for this variant, and the functional significance of the additional copy of this gene is currently unknown. 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: Oct 14, 2023