NM_001126108.2(SLC12A3):c.1670-1G>T AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 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:: RCV003559916.1

Allele description [Variation Report for NM_001126108.2(SLC12A3):c.1670-1G>T]

NM_001126108.2(SLC12A3):c.1670-1G>T

Gene:

SLC12A3:solute carrier family 12 member 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q13

Genomic location:

Preferred name:

NM_001126108.2(SLC12A3):c.1670-1G>T

HGVS:

NC_000016.10:g.56884048G>T
NG_009386.2:g.23842G>T
NM_000339.3:c.1670-1G>T
NM_001126107.2:c.1667-1G>T
NM_001126108.2:c.1670-1G>TMANE SELECT
NM_001410896.1:c.1667-1G>T
NC_000016.9:g.56917960G>T

Molecular consequence:

NM_000339.3:c.1670-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001126107.2:c.1667-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001126108.2:c.1670-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001410896.1:c.1667-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV004297743	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 21, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 15481849, 30596175, 17414160, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004297743

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 21, 2023)

germline

clinical testing

PubMed (4)
[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

A novel splice site mutation of the thiazide-sensitive NaCl cotransporter gene in a Japanese patient with Gitelman syndrome.

Iida K, Hanafusa M, Maekawa I, Kudo T, Takahashi K, Yoshioka S, Kishimoto M, Iguchi G, Tsukamoto T, Okimura Y, Kaji H, Chihara K.

Clin Nephrol. 2004 Sep;62(3):180-4.

PubMed [citation]

PMID:: 15481849

Clinical and Genetic Characteristics in Patients With Gitelman Syndrome.

Fujimura J, Nozu K, Yamamura T, Minamikawa S, Nakanishi K, Horinouchi T, Nagano C, Sakakibara N, Nakanishi K, Shima Y, Miyako K, Nozu Y, Morisada N, Nagase H, Ninchoji T, Kaito H, Iijima K.

Kidney Int Rep. 2019 Jan;4(1):119-125. doi: 10.1016/j.ekir.2018.09.015.

PubMed [citation]

PMID:: 30596175
PMCID:: PMC6308995

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV004297743.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change affects an acceptor splice site in intron 13 of the SLC12A3 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with Gitelman syndrome (PMID: 15481849, 17414160, 30596175). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. Studies have shown that disruption of this splice site results in skipping of exon 14, but is expected to preserve the integrity of the reading-frame (PMID: 17414160). 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: Feb 20, 2024

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