NM_015046.7(SETX):c.4020_4022del (p.Lys1341del) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 26, 2023
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:: RCV001858762.6

Allele description [Variation Report for NM_015046.7(SETX):c.4020_4022del (p.Lys1341del)]

NM_015046.7(SETX):c.4020_4022del (p.Lys1341del)

Gene:

SETX:senataxin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_015046.7(SETX):c.4020_4022del (p.Lys1341del)

HGVS:

NC_000009.12:g.132327578_132327580del
NG_007946.1:g.32408_32410del
NM_001351527.2:c.4020_4022del
NM_001351528.2:c.4020_4022del
NM_015046.7:c.4020_4022delMANE SELECT
NP_001338456.1:p.Lys1341del
NP_001338457.1:p.Lys1341del
NP_055861.3:p.Lys1341del
LRG_268t1:c.4020_4022del
LRG_268:g.32408_32410del
NC_000009.11:g.135202963_135202965del
NC_000009.11:g.135202965_135202967del
NM_015046.5:c.4020_4022del
NM_015046.5:c.4020_4022delGAA

Protein change:

K1341del

Links:

dbSNP: rs769558791

NCBI 1000 Genomes Browser:

rs769558791

Molecular consequence:

NM_001351527.2:c.4020_4022del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001351528.2:c.4020_4022del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_015046.7:c.4020_4022del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Amyotrophic lateral sclerosis type 4 (ALS4)
Synonyms:: AMYOTROPHIC LATERAL SCLEROSIS 4, JUVENILE; NEURONOPATHY, DISTAL HEREDITARY MOTOR, WITH PYRAMIDAL FEATURES
Identifiers:: MONDO: MONDO:0011223; MedGen: C1865409; Orphanet: 357043; OMIM: 602433

Name:: Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 (SCAN2)
Synonyms:: Ataxia-oculomotor apraxia 2; Ataxia-ocular apraxia-2; Ataxia with Oculomotor Apraxia
Identifiers:: MONDO: MONDO:0018996; MedGen: C1853761; Orphanet: 64753; OMIM: 606002

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002258270	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 26, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002258270

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 26, 2023)

germline

clinical testing

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002258270.3

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 805415). This variant has not been reported in the literature in individuals affected with SETX-related conditions. This variant is present in population databases (rs769558791, gnomAD 0.06%). This variant, c.4020_4022del, results in the deletion of 1 amino acid(s) of the SETX protein (p.Lys1341del), but otherwise preserves the integrity of the reading frame.

#	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: Sep 29, 2024

ClinVar

Relating variation to medicine