NM_015046.7(SETX):c.668T>A (p.Leu223His) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Oct 3, 2019
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:: RCV000992952.3

Allele description [Variation Report for NM_015046.7(SETX):c.668T>A (p.Leu223His)]

NM_015046.7(SETX):c.668T>A (p.Leu223His)

Gene:

SETX:senataxin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_015046.7(SETX):c.668T>A (p.Leu223His)

HGVS:

NC_000009.12:g.132336346A>T
NG_007946.1:g.23640T>A
NM_001351527.2:c.668T>A
NM_001351528.2:c.668T>A
NM_015046.7:c.668T>AMANE SELECT
NP_001338456.1:p.Leu223His
NP_001338457.1:p.Leu223His
NP_055861.3:p.Leu223His
LRG_268t1:c.668T>A
LRG_268:g.23640T>A
NC_000009.11:g.135211733A>T
NC_000009.11:g.135211733A>T
NM_015046.5:c.668T>A

Protein change:

L223H

Links:

dbSNP: rs1211053963

NCBI 1000 Genomes Browser:

rs1211053963

Molecular consequence:

NM_001351527.2:c.668T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001351528.2:c.668T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015046.7:c.668T>A - 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
SCV001145569	Athena Diagnostics Inc	criteria provided, single submitter (Athena Diagnostics Criteria)	Uncertain significance (Jan 16, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001992369	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Oct 3, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001145569

Athena Diagnostics Inc

criteria provided, single submitter

(Athena Diagnostics Criteria)

Uncertain significance
(Jan 16, 2019)

germline

clinical testing

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

SCV001992369

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Oct 3, 2019)

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	yes	not provided	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

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Athena Diagnostics Inc, SCV001145569.1

#	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, SCV001992369.2

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

Description

Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge

#	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 10, 2024

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