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NC_000002.12:g.(?_32126928)_(32128499_?)del AND Hereditary spastic paraplegia 4

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 3, 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:
RCV000560513.2

Allele description [Variation Report for NC_000002.12:g.(?_32126928)_(32128499_?)del]

NC_000002.12:g.(?_32126928)_(32128499_?)del

Gene:
SPAST:spastin [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p22.3
Genomic location:
Preferred name:
NC_000002.12:g.(?_32126928)_(32128499_?)del
HGVS:
  • NC_000002.12:g.(?_32126928)_(32128499_?)del
  • NC_000002.11:g.(?_32351997)_(32353568_?)del
  • NC_000002.11:g.(?_32351997)_(32353568_?)del
Links:

Condition(s)

Name:
Hereditary spastic paraplegia 4
Synonyms:
Spastic paraplegia 4, autosomal dominant; Familial spastic paraplegia autosomal dominant 2
Identifiers:
MONDO: MONDO:0008438; MedGen: C1866855; Orphanet: 100985; OMIM: 182601

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000645337Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Oct 3, 2022) 		germlineclinical testing

PubMed (3)
[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

Sequence variants in SPAST, SPG3A and HSPD1 in hereditary spastic paraplegia.

Svenstrup K, Bross P, Koefoed P, Hjermind LE, Eiberg H, Born AP, Vissing J, Gyllenborg J, Nørremølle A, Hasholt L, Nielsen JE.

J Neurol Sci. 2009 Sep 15;284(1-2):90-5. doi: 10.1016/j.jns.2009.04.024. Epub 2009 May 6.

PubMed [citation]
PMID:
19423133

The Alu-rich genomic architecture of SPAST predisposes to diverse and functionally distinct disease-associated CNV alleles.

Boone PM, Yuan B, Campbell IM, Scull JC, Withers MA, Baggett BC, Beck CR, Shaw CJ, Stankiewicz P, Moretti P, Goodwin WE, Hein N, Fink JK, Seong MW, Seo SH, Park SS, Karbassi ID, Batish SD, Ordóñez-Ugalde A, Quintáns B, Sobrido MJ, Stemmler S, et al.

Am J Hum Genet. 2014 Aug 7;95(2):143-61. doi: 10.1016/j.ajhg.2014.06.014. Epub 2014 Jul 24.

PubMed [citation]
PMID:
25065914
PMCID:
PMC4129405
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000645337.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 8-9 of the SPAST gene. This variant would be expected to be in-frame, preserving the integrity of the reading frame. A similar copy number variant has been observed in individuals with hereditary spastic paraplegia (PMID: 19423133, 25065914). It has also been observed to segregate with disease in related individuals. 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: Mar 26, 2023