NM_015046.7(SETX):c.3455T>G (p.Phe1152Cys) AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: Nov 26, 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:: RCV001705760.21

Allele description [Variation Report for NM_015046.7(SETX):c.3455T>G (p.Phe1152Cys)]

NM_015046.7(SETX):c.3455T>G (p.Phe1152Cys)

Gene:

SETX:senataxin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_015046.7(SETX):c.3455T>G (p.Phe1152Cys)

HGVS:

NC_000009.12:g.132328143A>C
NG_007946.1:g.31843T>G
NM_001351527.2:c.3455T>G
NM_001351528.2:c.3455T>G
NM_015046.7:c.3455T>GMANE SELECT
NP_001338456.1:p.Phe1152Cys
NP_001338457.1:p.Phe1152Cys
NP_055861.3:p.Phe1152Cys
NP_055861.3:p.Phe1152Cys
LRG_268t1:c.3455T>G
LRG_268:g.31843T>G
LRG_268p1:p.Phe1152Cys
NC_000009.11:g.135203530A>C
NM_015046.5:c.3455T>G
Q7Z333:p.Phe1152Cys

Protein change:

F1152C

Links:

UniProtKB: Q7Z333#VAR_018783; dbSNP: rs3739922

NCBI 1000 Genomes Browser:

rs3739922

Molecular consequence:

NM_001351527.2:c.3455T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001351528.2:c.3455T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015046.7:c.3455T>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000605092	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Nov 26, 2024)	germline	clinical testing	Citation Link,
SCV001870116	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Oct 17, 2018)	germline	clinical testing	Citation Link,
SCV005319227	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000605092

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)

Benign
(Nov 26, 2024)

germline

clinical testing

Citation Link,

SCV001870116

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Oct 17, 2018)

germline

clinical testing

Citation Link,

SCV005319227

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign

germline

not provided

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, not provided
not provided	germline	unknown	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 ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000605092.11

#	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 GeneDx, SCV001870116.1

#	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: 24694197)

#	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 Breakthrough Genomics, Breakthrough Genomics, SCV005319227.1

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

#	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: May 16, 2025

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