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NM_014946.4(SPAST):c.1238C>A (p.Ser413Ter) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 23, 2022
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:
RCV003482368.2

Allele description [Variation Report for NM_014946.4(SPAST):c.1238C>A (p.Ser413Ter)]

NM_014946.4(SPAST):c.1238C>A (p.Ser413Ter)

Gene:
SPAST:spastin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p22.3
Genomic location:
Preferred name:
NM_014946.4(SPAST):c.1238C>A (p.Ser413Ter)
HGVS:
  • NC_000002.12:g.32128472C>A
  • NG_008730.1:g.69862C>A
  • NM_001363823.2:c.1235C>A
  • NM_001363875.2:c.1139C>A
  • NM_001377959.1:c.1142C>A
  • NM_014946.3:c.1238C>A
  • NM_014946.4:c.1238C>AMANE SELECT
  • NM_199436.2:c.1142C>A
  • NP_001350752.1:p.Ser412Ter
  • NP_001350804.1:p.Ser380Ter
  • NP_001364888.1:p.Ser381Ter
  • NP_055761.2:p.Ser413Ter
  • NP_955468.1:p.Ser381Ter
  • LRG_714t1:c.1238C>A
  • LRG_714:g.69862C>A
  • NC_000002.11:g.32353541C>A
Protein change:
S380*
Links:
dbSNP: rs1553317045
NCBI 1000 Genomes Browser:
rs1553317045
Molecular consequence:
  • NM_001363823.2:c.1235C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001363875.2:c.1139C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001377959.1:c.1142C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_014946.4:c.1238C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_199436.2:c.1142C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004229187Athena Diagnostics
criteria provided, single submitter

(Athena Diagnostics Criteria)		Pathogenic
(Dec 23, 2022) 		unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Spastic paraplegia due to SPAST mutations is modified by the underlying mutation and sex.

Parodi L, Fenu S, Barbier M, Banneau G, Duyckaerts C, Tezenas du Montcel S, Monin ML, Ait Said S, Guegan J, Tallaksen CME, Sablonniere B, Brice A, Stevanin G, Depienne C, Durr A; SPATAX network..

Brain. 2018 Dec 1;141(12):3331-3342. doi: 10.1093/brain/awy285.

PubMed [citation]
PMID:
30476002

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, SCV004229187.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This variant is expected to result in the loss of a functional protein. Another nonsense variant in this codon (c.1238C>G) has been identified in at least one individual with spastic paraplegia. This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024