NM_014946.4(SPAST):c.1168A>G (p.Met390Val) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jul 14, 2024
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:: RCV000478313.3

Allele description [Variation Report for NM_014946.4(SPAST):c.1168A>G (p.Met390Val)]

NM_014946.4(SPAST):c.1168A>G (p.Met390Val)

Gene:

SPAST:spastin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p22.3

Genomic location:

Preferred name:

NM_014946.4(SPAST):c.1168A>G (p.Met390Val)

HGVS:

NC_000002.12:g.32127017A>G
NG_008730.1:g.68407A>G
NM_001363823.2:c.1165A>G
NM_001363875.2:c.1069A>G
NM_001377959.1:c.1072A>G
NM_014946.4:c.1168A>GMANE SELECT
NM_199436.2:c.1072A>G
NP_001350752.1:p.Met389Val
NP_001350804.1:p.Met357Val
NP_001364888.1:p.Met358Val
NP_055761.2:p.Met390Val
NP_055761.2:p.Met390Val
NP_955468.1:p.Met358Val
LRG_714t1:c.1168A>G
LRG_714:g.68407A>G
LRG_714p1:p.Met390Val
NC_000002.11:g.32352086A>G
NM_014946.3:c.1168A>G
Q9UBP0:p.Met390Val

Protein change:

M357V

Links:

UniProtKB: Q9UBP0#VAR_019441; dbSNP: rs797044850

NCBI 1000 Genomes Browser:

rs797044850

Molecular consequence:

NM_001363823.2:c.1165A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001363875.2:c.1069A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377959.1:c.1072A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_014946.4:c.1168A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_199436.2:c.1072A>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000568707	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jul 14, 2024)	germline	clinical testing	Citation Link,
SCV000615380	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Apr 28, 2017)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 20932283, 26208798, 14732620, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000568707

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jul 14, 2024)

germline

clinical testing

Citation Link,

SCV000615380

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Pathogenic
(Apr 28, 2017)

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	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

Mutational spectrum of the SPG4 (SPAST) and SPG3A (ATL1) genes in Spanish patients with hereditary spastic paraplegia.

Alvarez V, Sánchez-Ferrero E, Beetz C, Díaz M, Alonso B, Corao AI, Gámez J, Esteban J, Gonzalo JF, Pascual-Pascual SI, López de Munain A, Moris G, Ribacoba R, Márquez C, Rosell J, Marín R, García-Barcina MJ, Del Castillo E, Benito C, Coto E; Group for the Study of the Genetics of Spastic Paraplegia..

BMC Neurol. 2010 Oct 8;10:89. doi: 10.1186/1471-2377-10-89.

PubMed [citation]

PMID:: 20932283
PMCID:: PMC2964648

Mutational spectrum of the SPAST and ATL1 genes in Korean patients with hereditary spastic paraplegia.

Park H, Kang SH, Park S, Kim SY, Seo SH, Lee SJ, Lee JA, Cho SI, Sung JJ, Lee KW, Kim JY, Park SS, Seong MW.

J Neurol Sci. 2015 Oct 15;357(1-2):167-72. doi: 10.1016/j.jns.2015.07.024. Epub 2015 Jul 17.

PubMed [citation]

PMID:: 26208798

See all PubMed Citations (4)

Details of each submission

From GeneDx, SCV000568707.4

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 25525159, 26208798, 20932283, 14732620, 35076175, 32005694, 38168508, 37251230, 35982159, 33057194, 34983064, 12778437, 29691679, 21139634, 26094131)

#	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

From Athena Diagnostics, SCV000615380.1

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

#	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: Oct 8, 2024

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