NM_014946.4(SPAST):c.1507C>T (p.Arg503Trp) AND not provided

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

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Mar 17, 2022
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:: RCV000585136.26

Allele description

NM_014946.4(SPAST):c.1507C>T (p.Arg503Trp)

Gene:

SPAST:spastin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p22.3

Genomic location:

Preferred name:

NM_014946.4(SPAST):c.1507C>T (p.Arg503Trp)

HGVS:

NC_000002.12:g.32141917C>T
NG_008730.1:g.83307C>T
NM_001363823.2:c.1504C>T
NM_001363875.2:c.1408C>T
NM_001377959.1:c.1411C>T
NM_014946.4:c.1507C>TMANE SELECT
NM_199436.2:c.1411C>T
NP_001350752.1:p.Arg502Trp
NP_001350804.1:p.Arg470Trp
NP_001364888.1:p.Arg471Trp
NP_055761.2:p.Arg503Trp
NP_055761.2:p.Arg503Trp
NP_955468.1:p.Arg471Trp
LRG_714t1:c.1507C>T
LRG_714:g.83307C>T
LRG_714p1:p.Arg503Trp
NC_000002.11:g.32366986C>T
NM_014946.3:c.1507C>T
Q9UBP0:p.Arg503Trp

Protein change:

R470W

Links:

UniProtKB: Q9UBP0#VAR_026762; dbSNP: rs864622162

NCBI 1000 Genomes Browser:

rs864622162

Molecular consequence:

NM_001363823.2:c.1504C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363875.2:c.1408C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001377959.1:c.1411C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_014946.4:c.1507C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_199436.2:c.1411C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV000692984	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely pathogenic (Oct 1, 2017)	germline	clinical testing	Citation Link,
SCV002771042	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Likely pathogenic (Mar 17, 2022)	unknown	clinical testing	PubMed (10) [See all records that cite these PMIDs] 22960362, 24451228, 30476002, 32092540, 16055926, 16682546, 17594340, 18701882, 20932283, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000692984

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely pathogenic
(Oct 1, 2017)

germline

clinical testing

Citation Link,

SCV002771042

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Likely pathogenic
(Mar 17, 2022)

unknown

clinical testing

PubMed (10)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Novel and recurrent spastin mutations in a large series of SPG4 Italian families.

Nanetti L, Baratta S, Panzeri M, Tomasello C, Lovati C, Azzollini J, Gellera C, Di Bella D, Taroni F, Mariotti C.

Neurosci Lett. 2012 Oct 18;528(1):42-5. doi: 10.1016/j.neulet.2012.08.036. Epub 2012 Aug 25.

PubMed [citation]

PMID:: 22960362

Molecular epidemiology and clinical spectrum of hereditary spastic paraplegia in the Japanese population based on comprehensive mutational analyses.

Ishiura H, Takahashi Y, Hayashi T, Saito K, Furuya H, Watanabe M, Murata M, Suzuki M, Sugiura A, Sawai S, Shibuya K, Ueda N, Ichikawa Y, Kanazawa I, Goto J, Tsuji S.

J Hum Genet. 2014 Mar;59(3):163-72. doi: 10.1038/jhg.2013.139. Epub 2014 Jan 23.

PubMed [citation]

PMID:: 24451228

See all PubMed Citations (10)

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV000692984.26

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

#	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		1	not provided	not provided	not provided

From Athena Diagnostics, SCV002771042.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (10)

Description

The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant has been identified in multiple unrelated individuals with clinical features associated with this gene. Computational tools predict that this variant is damaging.

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

Last Updated: Jun 17, 2024

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