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NM_000343.4(SLC5A1):c.1765G>T (p.Glu589Ter) AND Congenital glucose-galactose malabsorption

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 29, 2021
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:
RCV001935874.6

Allele description [Variation Report for NM_000343.4(SLC5A1):c.1765G>T (p.Glu589Ter)]

NM_000343.4(SLC5A1):c.1765G>T (p.Glu589Ter)

Gene:
SLC5A1:solute carrier family 5 member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q12.3
Genomic location:
Preferred name:
NM_000343.4(SLC5A1):c.1765G>T (p.Glu589Ter)
HGVS:
  • NC_000022.11:g.32104885G>T
  • NG_017045.1:g.66854G>T
  • NM_000343.4:c.1765G>TMANE SELECT
  • NM_001256314.2:c.1384G>T
  • NP_000334.1:p.Glu589Ter
  • NP_001243243.1:p.Glu462Ter
  • NC_000022.10:g.32500872G>T
Protein change:
E462*
Links:
dbSNP: rs199727071
NCBI 1000 Genomes Browser:
rs199727071
Molecular consequence:
  • NM_000343.4:c.1765G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001256314.2:c.1384G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Congenital glucose-galactose malabsorption (GGM)
Synonyms:
Glucose galactose malabsorption deficiency; Carbohydrate intolerance of glucose galactose; Complex carbohydrate intolerance; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011731; MedGen: C0268186; Orphanet: 35710; OMIM: 606824

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002189477Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Apr 29, 2021) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Bitterness of glucose/galactose: novel mutations in the SLC5A1 gene.

Pode-Shakked B, Reish O, Aktuglu-Zeybek C, Kesselman D, Dekel B, Bujanover Y, Anikster Y.

J Pediatr Gastroenterol Nutr. 2014 Jan;58(1):57-60. doi: 10.1097/MPG.0000000000000114.

PubMed [citation]
PMID:
24048166

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, SCV002189477.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

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. This variant disrupts the C-terminus of the SLC5A1 protein. Other variant(s) that disrupt this region (p.Pro639Leufs*7) have been observed in individuals with SLC5A1-related conditions (PMID: 24048166). This suggests that this may be a clinically significant region of the protein. This variant has not been reported in the literature in individuals with SLC5A1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Glu589*) in the SLC5A1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 76 amino acid(s) of the SLC5A1 protein.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024