NM_025137.4(SPG11):c.5465_5477del (p.Phe1822fs) AND Hereditary spastic paraplegia 11

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 15, 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:: RCV000692085.5

Allele description [Variation Report for NM_025137.4(SPG11):c.5465_5477del (p.Phe1822fs)]

NM_025137.4(SPG11):c.5465_5477del (p.Phe1822fs)

Gene:

SPG11:SPG11 vesicle trafficking associated, spatacsin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

15q21.1

Genomic location:

Preferred name:

NM_025137.4(SPG11):c.5465_5477del (p.Phe1822fs)

HGVS:

NC_000015.10:g.44584208_44584220del
NC_000015.9:g.44876401_44876413del
NG_008885.1:g.84464_84476del
NM_001160227.2:c.5465_5477del
NM_025137.4:c.5465_5477delMANE SELECT
NP_001153699.1:p.Phe1822fs
NP_079413.3:p.Phe1822fs
NC_000015.9:g.44876401_44876413del
NC_000015.9:g.44876401_44876413delATCTGTCGAGAAA
NC_000015.9:g.44876406_44876418del
NM_025137.3:c.5465_5477delTTTCTCGACAGAT

Protein change:

F1822fs

Links:

dbSNP: rs1567138536

NCBI 1000 Genomes Browser:

rs1567138536

Molecular consequence:

NM_001160227.2:c.5465_5477del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_025137.4:c.5465_5477del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Hereditary spastic paraplegia 11
Synonyms:: SPASTIC PARAPLEGIA, AUTOSOMAL RECESSIVE, COMPLICATED, WITH THIN CORPUS CALLOSUM; SPASTIC PARAPLEGIA, AUTOSOMAL RECESSIVE, WITH MENTAL IMPAIRMENT AND THIN CORPUS CALLOSUM; Spastic paraplegia 11, autosomal recessive; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011445; MedGen: C1858479; Orphanet: 2822; OMIM: 604360

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000819892	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 15, 2018)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 19105190, 20110243, 22154821, 26556829, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000819892

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 15, 2018)

germline

clinical testing

PubMed (5)
[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

Screening of ARHSP-TCC patients expands the spectrum of SPG11 mutations and includes a large scale gene deletion.

Denora PS, Schlesinger D, Casali C, Kok F, Tessa A, Boukhris A, Azzedine H, Dotti MT, Bruno C, Truchetto J, Biancheri R, Fedirko E, Di Rocco M, Bueno C, Malandrini A, Battini R, Sickl E, de Leva MF, Boespflug-Tanguy O, Silvestri G, Simonati A, Said E, et al.

Hum Mutat. 2009 Mar;30(3):E500-19. doi: 10.1002/humu.20945.

PubMed [citation]

PMID:: 19105190

SPATACSIN mutations cause autosomal recessive juvenile amyotrophic lateral sclerosis.

Orlacchio A, Babalini C, Borreca A, Patrono C, Massa R, Basaran S, Munhoz RP, Rogaeva EA, St George-Hyslop PH, Bernardi G, Kawarai T.

Brain. 2010 Feb;133(Pt 2):591-8. doi: 10.1093/brain/awp325. Epub 2010 Jan 28.

PubMed [citation]

PMID:: 20110243
PMCID:: PMC2822627

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000819892.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Phe1822Serfs*12) in the SPG11 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SPG11-related disease. Loss-of-function variants in SPG11 are known to be pathogenic (PMID: 19105190, 20110243, 22154821, 26556829). 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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