NM_001365088.1(SLC12A6):c.1950dup (p.Leu651fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 15, 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:: RCV003669263.2

Allele description [Variation Report for NM_001365088.1(SLC12A6):c.1950dup (p.Leu651fs)]

NM_001365088.1(SLC12A6):c.1950dup (p.Leu651fs)

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.1950dup (p.Leu651fs)

HGVS:

NC_000015.10:g.34244071dup
NG_007951.1:g.98999dup
NM_001042494.2:c.1773dup
NM_001042495.2:c.1773dup
NM_001042496.2:c.1923dup
NM_001042497.2:c.1905dup
NM_001365088.1:c.1950dupMANE SELECT
NM_005135.2:c.1797dup
NM_133647.2:c.1950dup
NP_001035959.1:p.Leu592fs
NP_001035960.1:p.Leu592fs
NP_001035961.1:p.Leu642fs
NP_001035962.1:p.Leu636fs
NP_001352017.1:p.Leu651fs
NP_005126.1:p.Leu600fs
NP_598408.1:p.Leu651Serfs
NP_598408.1:p.Leu651fs
LRG_270t1:c.1797dup
LRG_270t2:c.1945dup
LRG_270:g.98999dup
LRG_270p1:p.Leu600fs
LRG_270p2:p.Leu651Serfs
NC_000015.9:g.34536266_34536267insA
NC_000015.9:g.34536272dup
NM_133647.1:c.1945dup
NM_133647.1:c.1950dupT

Protein change:

L592fs

Molecular consequence:

NM_001042494.2:c.1773dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001042495.2:c.1773dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001042496.2:c.1923dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001042497.2:c.1905dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001365088.1:c.1950dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_005135.2:c.1797dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_133647.2:c.1950dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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
SCV004387394	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 15, 2023)	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

SCV004387394

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 15, 2023)

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, SCV004387394.1

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

Description

This sequence change creates a premature translational stop signal (p.Leu651Serfs*68) 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). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SLC12A6-related conditions. ClinVar contains an entry for this variant (Variation ID: 1705184). For these reasons, this variant has been classified as Pathogenic.

#	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 26, 2024

ClinVar

Relating variation to medicine