NM_015046.7(SETX):c.3905G>A (p.Arg1302Gln) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 11, 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:: RCV002673510.2

Allele description [Variation Report for NM_015046.7(SETX):c.3905G>A (p.Arg1302Gln)]

NM_015046.7(SETX):c.3905G>A (p.Arg1302Gln)

Gene:

SETX:senataxin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_015046.7(SETX):c.3905G>A (p.Arg1302Gln)

HGVS:

NC_000009.12:g.132327693C>T
NG_007946.1:g.32293G>A
NM_001351527.2:c.3905G>A
NM_001351528.2:c.3905G>A
NM_015046.7:c.3905G>AMANE SELECT
NP_001338456.1:p.Arg1302Gln
NP_001338457.1:p.Arg1302Gln
NP_055861.3:p.Arg1302Gln
NP_055861.3:p.Arg1302Gln
LRG_268t1:c.3905G>A
LRG_268:g.32293G>A
LRG_268p1:p.Arg1302Gln
NC_000009.11:g.135203080C>T
NM_015046.5:c.3905G>A

Protein change:

R1302Q

Molecular consequence:

NM_001351527.2:c.3905G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001351528.2:c.3905G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015046.7:c.3905G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003546375	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Feb 11, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003546375

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Feb 11, 2022)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV003546375.2

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

Description

The c.3905G>A (p.R1302Q) alteration is located in exon 10 (coding exon 8) of the SETX gene. This alteration results from a G to A substitution at nucleotide position 3905, causing the arginine (R) at amino acid position 1302 to be replaced by a glutamine (Q). Based on data from the Genome Aggregation Database (gnomAD), the c.3905G>A alteration was observed in 0.0007% (2/282,714) of total alleles studied, with a frequency of 0.005% (1/19,952) in the East Asian subpopulation. The p.R1302 amino acid is not conserved in available vertebrate species. The p.R1302Q alteration is predicted to be tolerated by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

#	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 1, 2024

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