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NM_015046.7(SETX):c.2972T>C (p.Val991Ala) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 19, 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:
RCV003805682.1

Allele description

NM_015046.7(SETX):c.2972T>C (p.Val991Ala)

Gene:
SETX:senataxin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.13
Genomic location:
Preferred name:
NM_015046.7(SETX):c.2972T>C (p.Val991Ala)
HGVS:
  • NC_000009.12:g.132328626A>G
  • NG_007946.1:g.31360T>C
  • NM_001351527.2:c.2972T>C
  • NM_001351528.2:c.2972T>C
  • NM_015046.7:c.2972T>CMANE SELECT
  • NP_001338456.1:p.Val991Ala
  • NP_001338457.1:p.Val991Ala
  • NP_055861.3:p.Val991Ala
  • NP_055861.3:p.Val991Ala
  • LRG_268t1:c.2972T>C
  • LRG_268:g.31360T>C
  • LRG_268p1:p.Val991Ala
  • NC_000009.11:g.135204013A>G
  • NM_015046.5:c.2972T>C
Protein change:
V991A
Molecular consequence:
  • NM_001351527.2:c.2972T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351528.2:c.2972T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015046.7:c.2972T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Amyotrophic lateral sclerosis type 4 (ALS4)
Synonyms:
AMYOTROPHIC LATERAL SCLEROSIS 4, JUVENILE; NEURONOPATHY, DISTAL HEREDITARY MOTOR, WITH PYRAMIDAL FEATURES
Identifiers:
MONDO: MONDO:0011223; MedGen: C1865409; Orphanet: 357043; OMIM: 602433
Name:
Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 (SCAN2)
Synonyms:
Ataxia-oculomotor apraxia 2; Ataxia-ocular apraxia-2; Ataxia with Oculomotor Apraxia
Identifiers:
MONDO: MONDO:0018996; MedGen: C1853761; Orphanet: 64753; OMIM: 606002

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004591890Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Dec 19, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV004591890.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SETX protein function. This variant has not been reported in the literature in individuals affected with SETX-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces valine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 991 of the SETX protein (p.Val991Ala).

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

Last Updated: Mar 5, 2024