NM_014946.4(SPAST):c.1174-1G>C AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 26, 2018
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:: RCV000993060.2

Allele description [Variation Report for NM_014946.4(SPAST):c.1174-1G>C]

NM_014946.4(SPAST):c.1174-1G>C

Gene:

SPAST:spastin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p22.3

Genomic location:

Preferred name:

NM_014946.4(SPAST):c.1174-1G>C

HGVS:

NC_000002.12:g.32128407G>C
NG_008730.1:g.69797G>C
NM_001363823.2:c.1171-1G>C
NM_001363875.2:c.1075-1G>C
NM_001377959.1:c.1078-1G>C
NM_014946.4:c.1174-1G>CMANE SELECT
NM_199436.2:c.1078-1G>C
LRG_714t1:c.1174-1G>C
LRG_714:g.69797G>C
NC_000002.11:g.32353476G>C
NC_000002.11:g.32353476G>C
NM_014946.3:c.1174-1G>C

Links:

dbSNP: rs1553317024

NCBI 1000 Genomes Browser:

rs1553317024

Molecular consequence:

NM_001363823.2:c.1171-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001363875.2:c.1075-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001377959.1:c.1078-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_014946.4:c.1174-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_199436.2:c.1078-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV001145769	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Dec 26, 2018)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 20214791, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001145769

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Pathogenic
(Dec 26, 2018)

germline

clinical testing

PubMed (2)
[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

Unique spectrum of SPAST variants in Estonian HSP patients: presence of benign missense changes but lack of exonic rearrangements.

Braschinsky M, Tamm R, Beetz C, Sachez-Ferrero E, Raukas E, Lüüs SM, Gross-Paju K, Boillot C, Canzian F, Metspalu A, Haldre S.

BMC Neurol. 2010 Mar 9;10:17. doi: 10.1186/1471-2377-10-17.

PubMed [citation]

PMID:: 20214791
PMCID:: PMC2841126

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Athena Diagnostics, SCV001145769.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

The variant disrupts a canonical splice site, and is therefore predicted to result in the loss of a functional protein. Found in at least one symptomatic patient, and not found in general population data.

#	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: May 7, 2024

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