NM_015046.7(SETX):c.3950T>C (p.Val1317Ala) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 12, 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:: RCV000700419.7

Allele description [Variation Report for NM_015046.7(SETX):c.3950T>C (p.Val1317Ala)]

NM_015046.7(SETX):c.3950T>C (p.Val1317Ala)

Gene:

SETX:senataxin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_015046.7(SETX):c.3950T>C (p.Val1317Ala)

HGVS:

NC_000009.12:g.132327648A>G
NG_007946.1:g.32338T>C
NM_001351527.2:c.3950T>C
NM_001351528.2:c.3950T>C
NM_015046.7:c.3950T>CMANE SELECT
NP_001338456.1:p.Val1317Ala
NP_001338457.1:p.Val1317Ala
NP_055861.3:p.Val1317Ala
LRG_268t1:c.3950T>C
LRG_268:g.32338T>C
NC_000009.11:g.135203035A>G
NM_015046.5:c.3950T>C

Protein change:

V1317A

Links:

dbSNP: rs1564539968

NCBI 1000 Genomes Browser:

rs1564539968

Molecular consequence:

NM_001351527.2:c.3950T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001351528.2:c.3950T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_015046.7:c.3950T>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000829173	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 12, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000829173

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 12, 2022)

germline

clinical testing

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

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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000829173.4

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

Description

ClinVar contains an entry for this variant (Variation ID: 577618). This sequence change replaces valine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 1317 of the SETX protein (p.Val1317Ala). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SETX-related conditions. 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. 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.

#	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: Sep 29, 2024

ClinVar

Relating variation to medicine