NM_015046.7(SETX):c.5927T>G (p.Leu1976Arg) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Apr 28, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001781169.6

Allele description [Variation Report for NM_015046.7(SETX):c.5927T>G (p.Leu1976Arg)]

NM_015046.7(SETX):c.5927T>G (p.Leu1976Arg)

Gene:

SETX:senataxin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_015046.7(SETX):c.5927T>G (p.Leu1976Arg)

HGVS:

NC_000009.12:g.132296909A>C
NG_007946.1:g.63077T>G
NM_001351527.2:c.5927T>G
NM_001351528.2:c.5927T>G
NM_015046.7:c.5927T>GMANE SELECT
NP_001338456.1:p.Leu1976Arg
NP_001338457.1:p.Leu1976Arg
NP_055861.3:p.Leu1976Arg
NP_055861.3:p.Leu1976Arg
LRG_268t1:c.5927T>G
LRG_268:g.63077T>G
LRG_268p1:p.Leu1976Arg
NC_000009.11:g.135172296A>C
NM_015046.5:c.5927T>G
NM_015046.5:c.5927T>G
NM_015046.6:c.5927T>G
Q7Z333:p.Leu1976Arg

Protein change:

L1976R; LEU1976ARG

Links:

UniProtKB: Q7Z333#VAR_072588; OMIM: 608465.0009; dbSNP: rs121434379

NCBI 1000 Genomes Browser:

rs121434379

Molecular consequence:

NM_001351527.2:c.5927T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001351528.2:c.5927T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015046.7:c.5927T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002020080	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 19, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002513081	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 28, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002020080

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 19, 2021)

germline

clinical testing

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

SCV002513081

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Apr 28, 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
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Revvity Omics, Revvity, SCV002020080.3

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

#	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

From GeneDx, SCV002513081.2

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25116135, 17159128, 23129421, 33333218, 33397523, 20301333, 19697368, 17720498, 15732101)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 16, 2024

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