NM_000342.4(SLC4A1):c.1898C>T (p.Ser633Leu) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 22, 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:: RCV003734677.2

Allele description [Variation Report for NM_000342.4(SLC4A1):c.1898C>T (p.Ser633Leu)]

NM_000342.4(SLC4A1):c.1898C>T (p.Ser633Leu)

Gene:

SLC4A1:solute carrier family 4 member 1 (Diego blood group) [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.31

Genomic location:

Preferred name:

NM_000342.4(SLC4A1):c.1898C>T (p.Ser633Leu)

HGVS:

NC_000017.11:g.44254655G>A
NG_007498.1:g.18480C>T
NM_000342.4:c.1898C>TMANE SELECT
NP_000333.1:p.Ser633Leu
LRG_803t1:c.1898C>T
LRG_803:g.18480C>T
LRG_803p1:p.Ser633Leu
NC_000017.10:g.42332023G>A

Protein change:

S633L

Molecular consequence:

NM_000342.4:c.1898C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV004539133	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 22, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31949730, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004539133

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 22, 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

Clinical features and genetic findings in Chinese children with distal renal tubular acidosis.

Zhou F, Mao J, Ye Q, Zhu X, Zhang Y, Ye Y, Fu H, Shen H, Lu Z, Xia Y, Liu A, Shu Q, Du L.

Int J Clin Exp Pathol. 2018;11(7):3523-3532.

PubMed [citation]

PMID:: 31949730
PMCID:: PMC6962865

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, SCV004539133.1

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

Description

This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 633 of the SLC4A1 protein (p.Ser633Leu). This variant is present in population databases (rs760240566, gnomAD 0.003%). This missense change has been observed in individual(s) with renal tubular acidosis (PMID: 31949730). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. 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 SLC4A1 protein function with a negative predictive value of 80%. 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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