NM_015087.5(SPART):c.1294del (p.Ser432fs) AND not provided

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 22, 2020
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:: RCV001382087.6

Allele description

NM_015087.5(SPART):c.1294del (p.Ser432fs)

Gene:

SPART:spartin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

13q13.3

Genomic location:

Preferred name:

NM_015087.5(SPART):c.1294del (p.Ser432fs)

HGVS:

NC_000013.11:g.36314417del
NG_011559.2:g.60765del
NM_001142294.2:c.1294del
NM_001142295.2:c.1294del
NM_001142296.2:c.1294del
NM_015087.5:c.1294delMANE SELECT
NP_001135766.1:p.Ser432fs
NP_001135767.1:p.Ser432fs
NP_001135768.1:p.Ser432fs
NP_055902.1:p.Ser432fs
NC_000013.10:g.36888553del
NC_000013.10:g.36888554del

Protein change:

S432fs

Links:

dbSNP: rs2137335988

NCBI 1000 Genomes Browser:

rs2137335988

Molecular consequence:

NM_001142294.2:c.1294del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142295.2:c.1294del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142296.2:c.1294del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015087.5:c.1294del - 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
SCV001580717	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 22, 2020)	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

SCV001580717

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 22, 2020)

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, SCV001580717.5

#	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 SPART are known to be pathogenic (PMID: 18413476, 20437587, 20504295). This variant has not been reported in the literature in individuals with SPART-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Ser432Profs*3) in the SPART 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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