NM_015087.5(SPART):c.696dup (p.Val233fs) AND not provided

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

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Nov 19, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002571603.3

Allele description

NM_015087.5(SPART):c.696dup (p.Val233fs)

Gene:

SPART:spartin [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

13q13.3

Genomic location:

Preferred name:

NM_015087.5(SPART):c.696dup (p.Val233fs)

HGVS:

NC_000013.11:g.36335142dup
NG_011559.2:g.40046dup
NM_001142294.2:c.696dup
NM_001142295.2:c.696dup
NM_001142296.2:c.696dup
NM_015087.4:c.696dup
NM_015087.5:c.696dupMANE SELECT
NP_001135766.1:p.Val233fs
NP_001135767.1:p.Val233fs
NP_001135768.1:p.Val233fs
NP_055902.1:p.Val233fs
NC_000013.10:g.36909271_36909272insA
NC_000013.10:g.36909279dup
NM_015087.4:c.696dupT

Protein change:

V233fs

Molecular consequence:

NM_001142294.2:c.696dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142295.2:c.696dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142296.2:c.696dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015087.5:c.696dup - 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
SCV003449446	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 19, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 18413476, 20437587, 20504295, 28492532
SCV004030585	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Feb 27, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003449446

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 19, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV004030585

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Feb 27, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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, SCV003449446.2

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

Description

This sequence change creates a premature translational stop signal (p.Val233Cysfs*8) in the SPART gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SPART are known to be pathogenic (PMID: 18413476, 20437587, 20504295). This variant is present in population databases (rs770560051, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with SPART-related conditions. ClinVar contains an entry for this variant (Variation ID: 1878642). 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

From GeneDx, SCV004030585.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 9, 2024

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