NM_005982.4(SIX1):c.397_399del (p.Glu133del) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 21, 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:: RCV003162220.1

Allele description [Variation Report for NM_005982.4(SIX1):c.397_399del (p.Glu133del)]

NM_005982.4(SIX1):c.397_399del (p.Glu133del)

Gene:

SIX1:SIX homeobox 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

14q23.1

Genomic location:

Preferred name:

NM_005982.4(SIX1):c.397_399del (p.Glu133del)

Other names:

E133delE

HGVS:

NC_000014.9:g.60648793_60648795del
NG_008231.1:g.5645_5647del
NM_005982.4:c.397_399delMANE SELECT
NP_005973.1:p.Glu133del
NC_000014.8:g.61115509_61115511del
NC_000014.8:g.61115511_61115513del
NM_005982.2:c.397_399del
NM_005982.3:c.397_399del

Protein change:

E133del

Links:

OMIM: 601205.0003; dbSNP: rs80356460

NCBI 1000 Genomes Browser:

rs80356460

Molecular consequence:

NM_005982.4:c.397_399del - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV003915023	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 21, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003915023

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 21, 2023)

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

Details of each submission

From GeneDx, SCV003915023.1

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

Description

Functional studies demonstrate a damaging effect; variant results in diminished DNA binding and decreased lacZ activity (Ruf RG et al., 2004; Patrick AN et al., 2009); In-frame deletion of 1 amino acid in a non-repeat region; Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 15141091, 19497856, 33105617, 31595699)

#	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 5, 2024

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