NM_001365088.1(SLC12A6):c.752dup (p.Ser252fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 5, 2021
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:: RCV001860481.4

Allele description [Variation Report for NM_001365088.1(SLC12A6):c.752dup (p.Ser252fs)]

NM_001365088.1(SLC12A6):c.752dup (p.Ser252fs)

Gene:

SLC12A6:solute carrier family 12 member 6 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

15q14

Genomic location:

Preferred name:

NM_001365088.1(SLC12A6):c.752dup (p.Ser252fs)

HGVS:

NC_000015.10:g.34255390dup
NG_007951.1:g.87679dup
NM_001042494.2:c.575dup
NM_001042495.2:c.575dup
NM_001042496.2:c.725dup
NM_001042497.2:c.707dup
NM_001365088.1:c.752dupMANE SELECT
NM_005135.2:c.599dup
NM_133647.2:c.752dup
NP_001035959.1:p.Ser193fs
NP_001035960.1:p.Ser193fs
NP_001035961.1:p.Ser243fs
NP_001035962.1:p.Ser237fs
NP_001352017.1:p.Ser252fs
NP_005126.1:p.Ser201fs
NP_598408.1:p.Ser252fs
LRG_270t1:c.599dup
LRG_270:g.87679dup
LRG_270p1:p.Ser201fs
NC_000015.9:g.34547586_34547587insC
NC_000015.9:g.34547591dup
NM_133647.1:c.752dupG

Protein change:

S193fs

Links:

dbSNP: rs1555380716

NCBI 1000 Genomes Browser:

rs1555380716

Molecular consequence:

NM_001042494.2:c.575dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001042495.2:c.575dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001042496.2:c.725dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001042497.2:c.707dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001365088.1:c.752dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_005135.2:c.599dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_133647.2:c.752dup - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV002118787	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 5, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 12368912, 16606917, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002118787

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 5, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

The K-Cl cotransporter KCC3 is mutant in a severe peripheral neuropathy associated with agenesis of the corpus callosum.

Howard HC, Mount DB, Rochefort D, Byun N, Dupré N, Lu J, Fan X, Song L, Rivière JB, Prévost C, Horst J, Simonati A, Lemcke B, Welch R, England R, Zhan FQ, Mercado A, Siesser WB, George AL Jr, McDonald MP, Bouchard JP, Mathieu J, et al.

Nat Genet. 2002 Nov;32(3):384-92. Epub 2002 Oct 7. Erratum in: Nat Genet 2002 Dec;32(4):681.

PubMed [citation]

PMID:: 12368912

Novel truncating and missense mutations of the KCC3 gene associated with Andermann syndrome.

Uyanik G, Elcioglu N, Penzien J, Gross C, Yilmaz Y, Olmez A, Demir E, Wahl D, Scheglmann K, Winner B, Bogdahn U, Topaloglu H, Hehr U, Winkler J.

Neurology. 2006 Apr 11;66(7):1044-8. Erratum in: Neurology. 2006 Oct 24;67(8):1528.

PubMed [citation]

PMID:: 16606917

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002118787.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with SLC12A6-related conditions. ClinVar contains an entry for this variant (Variation ID: 523557). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Ser252Leufs*38) in the SLC12A6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC12A6 are known to be pathogenic (PMID: 12368912, 16606917).

#	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: Oct 8, 2024

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