NM_001126108.2(SLC12A3):c.1723A>G (p.Ile575Val) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 21, 2022
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:: RCV002928410.2

Allele description [Variation Report for NM_001126108.2(SLC12A3):c.1723A>G (p.Ile575Val)]

NM_001126108.2(SLC12A3):c.1723A>G (p.Ile575Val)

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.1723A>G (p.Ile575Val)

HGVS:

NC_000016.10:g.56884102A>G
NG_009386.2:g.23896A>G
NM_000339.3:c.1723A>G
NM_001126107.2:c.1720A>G
NM_001126108.2:c.1723A>GMANE SELECT
NM_001410896.1:c.1720A>G
NP_000330.3:p.Ile575Val
NP_001119579.2:p.Ile574Val
NP_001119580.2:p.Ile575Val
NP_001397825.1:p.Ile574Val
NC_000016.9:g.56918014A>G
NM_000339.2:c.1723A>G

Protein change:

I574V

Molecular consequence:

NM_000339.3:c.1723A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001126107.2:c.1720A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001126108.2:c.1723A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001410896.1:c.1720A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Homo sapiens chromosome 8, GRCh38.p14 Primary Assembly
Homo sapiens chromosome 8, GRCh38.p14 Primary Assembly
gi|568815590|gnl|ASM:GCF_000001305| |NC_000008.11||gpp|GPC_000001300.1||gnl|NCBI_GENOMES|8

Nucleotide
deoxyribonuclease TATDN1 isoform X1 [Homo sapiens]
deoxyribonuclease TATDN1 isoform X1 [Homo sapiens]
gi|2462497276|ref|XP_054189019.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003266900	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 21, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003266900

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 21, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

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, SCV003266900.1

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

Description

This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 575 of the SLC12A3 protein (p.Ile575Val). This variant is present in population databases (rs772849642, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with SLC12A3-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SLC12A3 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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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