NM_000339.2(SLC12A3):c.-1471_894del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 15, 2019
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:: RCV001216229.10

Allele description [Variation Report for NM_000339.2(SLC12A3):c.-1471_894del]

NM_000339.2(SLC12A3):c.-1471_894del

Genes:

LOC130059053:ATAC-STARR-seq lymphoblastoid active region 10855 [Gene]
LOC130059054:ATAC-STARR-seq lymphoblastoid active region 10856 [Gene]
SLC12A3:solute carrier family 12 member 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q13

Genomic location:

Preferred name:

NM_000339.2(SLC12A3):c.-1471_894del

HGVS:

NC_000016.10:g.56863765_56872392del
NG_009386.2:g.3559_12186del
NC_000016.9:g.56897677_56906304del
NM_000339.2:c.-1471_894del

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
SCV001388015	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 15, 2019)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 21757836, 10616841, 21628937, 26041598, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001388015

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 15, 2019)

germline

clinical testing

PubMed (5)
[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 case of Gitelman syndrome associated with idiopathic intracranial hypertension.

Tsutsui H, Hamano T, Kawaura Y, Inaba S, Miyamori I, Yasujima M, Yoneda M, Kuriyama M.

Intern Med. 2011;50(14):1493-6. Epub 2011 Jul 15.

PubMed [citation]

PMID:: 21757836

Novel mutations in thiazide-sensitive Na-Cl cotransporter gene of patients with Gitelman's syndrome.

Monkawa T, Kurihara I, Kobayashi K, Hayashi M, Saruta T.

J Am Soc Nephrol. 2000 Jan;11(1):65-70. doi: 10.1681/ASN.V11165.

PubMed [citation]

PMID:: 10616841

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001388015.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This variant is a deletion of the genomic region encompassing 1-6 and part of exon 7 (c.-1471_894del) of the SLC12A3 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with SLC12A3-related conditions. This variant disrupts the p.Thr180 amino acid residue in SLC12A3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10616841, 21628937, 26041598, 21757836). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Loss-of-function variants in SLC12A3 are known to be pathogenic (PMID: 20848653, 22009145, 25841442). 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: Apr 20, 2024

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