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NM_015046.7(SETX):c.5820del (p.Ala1941fs) AND Inborn genetic diseases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 27, 2020
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:
RCV002353162.2

Allele description [Variation Report for NM_015046.7(SETX):c.5820del (p.Ala1941fs)]

NM_015046.7(SETX):c.5820del (p.Ala1941fs)

Gene:
SETX:senataxin [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q34.13
Genomic location:
Preferred name:
NM_015046.7(SETX):c.5820del (p.Ala1941fs)
HGVS:
  • NC_000009.12:g.132297018del
  • NG_007946.1:g.62970del
  • NM_001351527.2:c.5820del
  • NM_001351528.2:c.5820del
  • NM_015046.7:c.5820delMANE SELECT
  • NP_001338456.1:p.Ala1941fs
  • NP_001338457.1:p.Ala1941fs
  • NP_055861.3:p.Ala1941Glnfs
  • NP_055861.3:p.Ala1941fs
  • LRG_268t1:c.5818del
  • LRG_268:g.62970del
  • LRG_268p1:p.Ala1941Glnfs
  • NC_000009.11:g.135172405del
  • NM_015046.5:c.5818delA
  • NM_015046.5:c.5820delA
Protein change:
A1941fs
Molecular consequence:
  • NM_001351527.2:c.5820del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351528.2:c.5820del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_015046.7:c.5820del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002653459Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Feb 27, 2020) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV002653459.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.5820delA variant, located in coding exon 12 of the SETX gene, results from a deletion of one nucleotide at nucleotide position 5820, causing a translational frameshift with a predicted alternate stop codon (p.A1941Qfs*2). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

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

Last Updated: May 1, 2024