NM_015087.5(SPART):c.475_476del (p.Leu159fs) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 3, 2019
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:: RCV001376632.4

Allele description

NM_015087.5(SPART):c.475_476del (p.Leu159fs)

Gene:

SPART:spartin [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

13q13.3

Genomic location:

Preferred name:

NM_015087.5(SPART):c.475_476del (p.Leu159fs)

HGVS:

NC_000013.11:g.36335356GA[1]
NG_011559.2:g.39823CT[1]
NM_001142294.2:c.475_476del
NM_001142295.2:c.475_476del
NM_001142296.2:c.475_476del
NM_015087.5:c.475_476delMANE SELECT
NP_001135766.1:p.Leu159fs
NP_001135767.1:p.Leu159fs
NP_001135768.1:p.Leu159fs
NP_055902.1:p.Leu159fs
NC_000013.10:g.36909492_36909493del
NC_000013.10:g.36909493GA[1]
NM_015087.4:c.475_476del
NM_015087.4:c.475_476delCT

Protein change:

L159fs

Links:

dbSNP: rs1480709252

NCBI 1000 Genomes Browser:

rs1480709252

Molecular consequence:

NM_001142294.2:c.475_476del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142295.2:c.475_476del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142296.2:c.475_476del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015087.5:c.475_476del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001225279	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 3, 2019)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 18413476, 20437587, 20504295, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001225279

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 3, 2019)

germline

clinical testing

PubMed (4)
[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

Lack of spartin protein in Troyer syndrome: a loss-of-function disease mechanism?

Bakowska JC, Wang H, Xin B, Sumner CJ, Blackstone C.

Arch Neurol. 2008 Apr;65(4):520-4. doi: 10.1001/archneur.65.4.520.

PubMed [citation]

PMID:: 18413476
PMCID:: PMC5580255

Developmental and degenerative features in a complicated spastic paraplegia.

Manzini MC, Rajab A, Maynard TM, Mochida GH, Tan WH, Nasir R, Hill RS, Gleason D, Al Saffar M, Partlow JN, Barry BJ, Vernon M, LaMantia AS, Walsh CA.

Ann Neurol. 2010 Apr;67(4):516-25. doi: 10.1002/ana.21923.

PubMed [citation]

PMID:: 20437587
PMCID:: PMC3027847

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001225279.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in SPG20 are known to be pathogenic (PMID: 18413476, 20437587, 20504295). This variant has not been reported in the literature in individuals with SPG20-related conditions. ClinVar contains an entry for this variant (Variation ID: 631700). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Leu159Valfs*21) in the SPG20 gene. It is expected to result in an absent or disrupted protein product.

#	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: Jun 9, 2024

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