NM_015046.7(SETX):c.472T>G (p.Leu158Val) AND not provided

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Oct 1, 2024
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:: RCV000513524.47

Allele description [Variation Report for NM_015046.7(SETX):c.472T>G (p.Leu158Val)]

NM_015046.7(SETX):c.472T>G (p.Leu158Val)

Gene:

SETX:senataxin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_015046.7(SETX):c.472T>G (p.Leu158Val)

HGVS:

NC_000009.12:g.132342716A>C
NG_007946.1:g.17270T>G
NM_001351527.2:c.472T>G
NM_001351528.2:c.472T>G
NM_015046.7:c.472T>GMANE SELECT
NP_001338456.1:p.Leu158Val
NP_001338457.1:p.Leu158Val
NP_055861.3:p.Leu158Val
LRG_268t1:c.472T>G
LRG_268:g.17270T>G
NC_000009.11:g.135218103A>C
NM_015046.5:c.472T>G

Protein change:

L158V

Links:

dbSNP: rs145438764

NCBI 1000 Genomes Browser:

rs145438764

Molecular consequence:

NM_001351527.2:c.472T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001351528.2:c.472T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015046.7:c.472T>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000565556	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Apr 19, 2021)	germline	clinical testing	Citation Link,
SCV000605100	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Likely benign (Nov 29, 2023)	germline	clinical testing	Citation Link,
SCV000609358	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Oct 1, 2024)	germline	clinical testing	Citation Link,
SCV000615191	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Nov 30, 2018)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 25174650, 25382069, 27013921, 26467025

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	25	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutation analysis of patients with neurodegenerative disorders using NeuroX array.

Ghani M, Lang AE, Zinman L, Nacmias B, Sorbi S, Bessi V, Tedde A, Tartaglia MC, Surace EI, Sato C, Moreno D, Xi Z, Hung R, Nalls MA, Singleton A, St George-Hyslop P, Rogaeva E.

Neurobiol Aging. 2015 Jan;36(1):545.e9-14. doi: 10.1016/j.neurobiolaging.2014.07.038. Epub 2014 Aug 1.

PubMed [citation]

PMID:: 25174650
PMCID:: PMC4268030

Amyotrophic lateral sclerosis onset is influenced by the burden of rare variants in known amyotrophic lateral sclerosis genes.

Cady J, Allred P, Bali T, Pestronk A, Goate A, Miller TM, Mitra RD, Ravits J, Harms MB, Baloh RH.

Ann Neurol. 2015 Jan;77(1):100-13. doi: 10.1002/ana.24306. Epub 2014 Nov 27.

PubMed [citation]

PMID:: 25382069
PMCID:: PMC4293318

See all PubMed Citations (4)

Details of each submission

From GeneDx, SCV000565556.3

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

Description

This variant is associated with the following publications: (PMID: 25174650, 25382069, 27013921, 29525178)

#	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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000605100.7

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

#	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 CeGaT Center for Human Genetics Tuebingen, SCV000609358.32

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	25	not provided	not provided	clinical testing	not provided

Description

SETX: BS2

#	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		25	not provided	not provided	not provided

From Athena Diagnostics, SCV000615191.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

#	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: Jan 13, 2025

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