NM_001126108.2(SLC12A3):c.2598_2599delinsTA (p.Gly867Ser) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 26, 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:: RCV003819762.2

Allele description [Variation Report for NM_001126108.2(SLC12A3):c.2598_2599delinsTA (p.Gly867Ser)]

NM_001126108.2(SLC12A3):c.2598_2599delinsTA (p.Gly867Ser)

Gene:

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

Variant type:

Indel

Cytogenetic location:

16q13

Genomic location:

Preferred name:

NM_001126108.2(SLC12A3):c.2598_2599delinsTA (p.Gly867Ser)

HGVS:

NC_000016.10:g.56894607_56894608delinsTA
NG_009386.2:g.34401_34402delinsTA
NM_000339.3:c.2625_2626delinsTA
NM_001126107.2:c.2622_2623delinsTA
NM_001126108.2:c.2598_2599delinsTAMANE SELECT
NM_001410896.1:c.2595_2596delinsTA
NP_000330.3:p.Gly876Ser
NP_001119579.2:p.Gly875Ser
NP_001119580.2:p.Gly867Ser
NP_001397825.1:p.Gly866Ser
NC_000016.9:g.56928519_56928520delinsTA

Protein change:

G866S

Molecular consequence:

NM_000339.3:c.2625_2626delinsTA - missense variant - [Sequence Ontology: SO:0001583]
NM_001126107.2:c.2622_2623delinsTA - missense variant - [Sequence Ontology: SO:0001583]
NM_001126108.2:c.2598_2599delinsTA - missense variant - [Sequence Ontology: SO:0001583]
NM_001410896.1:c.2595_2596delinsTA - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Mus musculus Fanconi anemia, complementation group M (Fancm), transcript variant...
Mus musculus Fanconi anemia, complementation group M (Fancm), transcript variant 2, mRNA
gi|1402624440|ref|NM_001364447.1|

Nucleotide
PREDICTED: Homo sapiens chromosome 10 open reading frame 67 (C10orf67), transcri...
PREDICTED: Homo sapiens chromosome 10 open reading frame 67 (C10orf67), transcript variant X2, mRNA
gi|2462518281|ref|XM_054365423.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004617722	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Sep 26, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 17654016, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004617722

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Sep 26, 2023)

germline

clinical testing

PubMed (2)
[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

Novel mutations in the SLC12A3 gene causing Gitelman's syndrome in Swedes.

Fava C, Montagnana M, Rosberg L, Burri P, Jönsson A, Wanby P, Wahrenberg H, Hulthén UL, Aurell M, Guidi GC, Melander O.

DNA Seq. 2007 Oct;18(5):395-9.

PubMed [citation]

PMID:: 17654016

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004617722.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

A different variant (c.2626G>A ) giving rise to the same protein effect has been determined to be pathogenic (PMID: 17654016; Invitae). This suggests that this variant is also likely to be causative of disease. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 876 of the SLC12A3 protein (p.Gly876Ser).

#	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: Sep 29, 2024

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