SLC5A2

solute carrier family 5 member 2, the group of Solute carrier family 5

Basic information

Region (hg38): 16:31483002-31490860

Previous symbols: [ "SGLT2" ]

Links

ENSG00000140675NCBI:6524OMIM:182381HGNC:11037Uniprot:P31639AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • familial renal glucosuria (Supportive), mode of inheritance: AD
  • familial renal glucosuria (Strong), mode of inheritance: AR
  • familial renal glucosuria (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Renal glucosuriaAD/ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingRenal12436245; 21165652

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC5A2 gene.

  • Familial renal glucosuria (2 variants)
  • SLC5A2-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC5A2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
11
clinvar
5
clinvar
2
clinvar
18
missense
3
clinvar
95
clinvar
2
clinvar
1
clinvar
101
nonsense
2
clinvar
2
start loss
0
frameshift
2
clinvar
6
clinvar
8
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
2
splice region
1
6
5
12
non coding
7
clinvar
4
clinvar
3
clinvar
14
Total 2 12 116 11 6

Highest pathogenic variant AF is 0.0000723

Variants in SLC5A2

This is a list of pathogenic ClinVar variants found in the SLC5A2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
16-31483140-G-A Inborn genetic diseases Uncertain significance (Dec 03, 2021)2264460
16-31483155-G-A Familial renal glucosuria Uncertain significance (Jan 13, 2018)886662
16-31483162-C-T Familial renal glucosuria Uncertain significance (Jan 12, 2018)319053
16-31483188-G-C Inborn genetic diseases Uncertain significance (Dec 03, 2021)2364775
16-31483196-T-C Familial renal glucosuria Benign (Dec 31, 2019)777013
16-31483222-T-C Inborn genetic diseases Uncertain significance (Mar 21, 2024)3320044
16-31484350-G-C Benign (Nov 12, 2018)1241803
16-31484655-C-G SLC5A2-related disorder Likely benign (Apr 25, 2019)3047822
16-31484657-C-A Familial renal glucosuria Pathogenic (Mar 01, 2011)29880
16-31484698-C-T Familial renal glucosuria Uncertain significance (Jan 12, 2018)886663
16-31484709-T-C SLC5A2-related disorder Uncertain significance (May 01, 2023)2633293
16-31484717-GGCAGGACGCA-G Uncertain significance (Sep 16, 2018)591648
16-31484724-C-T SLC5A2-related disorder Uncertain significance (Feb 10, 2024)3036114
16-31484731-TG-T Uncertain significance (Sep 16, 2018)591555
16-31484736-T-G Uncertain significance (Mar 10, 2023)2579624
16-31484743-C-T Familial renal glucosuria Uncertain significance (Nov 08, 2021)3061899
16-31484846-A-G Familial renal glucosuria Uncertain significance (Apr 29, 2022)2502154
16-31484847-T-A Familial renal glucosuria Uncertain significance (Aug 15, 2019)829885
16-31484874-C-A Inborn genetic diseases Uncertain significance (Feb 22, 2023)2487516
16-31484885-G-A Familial renal glucosuria Pathogenic (Aug 02, 2016)253135
16-31484914-C-A Familial renal glucosuria Pathogenic (Mar 01, 2011)29882
16-31484915-G-C Uncertain significance (May 28, 2021)1326666
16-31484914-C-CTT Familial renal glucosuria Likely pathogenic (Jun 20, 2019)804477
16-31485730-C-T Familial renal glucosuria Uncertain significance (Apr 04, 2024)3067930
16-31485731-G-A SLC5A2-related disorder Likely benign (Jan 17, 2020)3051410

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC5A2protein_codingprotein_codingENST00000330498 147859
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.92e-140.17912563901091257480.000434
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.164724061.160.00002584262
Missense in Polyphen208197.171.05492064
Synonymous-2.182181811.210.00001261440
Loss of Function1.022430.00.7990.00000143323

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001220.00122
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.0001470.000139
European (Non-Finnish)0.0005830.000571
Middle Eastern0.0001090.000109
South Asian0.0002940.000294
Other0.001140.00114

dbNSFP

Source: dbNSFP

Function
FUNCTION: Sodium-dependent glucose transporter. Has a Na(+) to glucose coupling ratio of 1:1.;
Disease
DISEASE: Renal glucosuria (GLYS) [MIM:233100]: A disorder characterized by persistent isolated glucosuria, normal fasting serum glucose concentration, decreased renal tubular resorption of glucose from the urine, and absence of any other signs of tubular dysfunction. {ECO:0000269|PubMed:14614622}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Nuclear Receptors Meta-Pathway;NRF2 pathway;SLC-mediated transmembrane transport;Transport of small molecules;Fructose and mannose metabolism;Galactose metabolism;Cellular hexose transport (Consensus)

Recessive Scores

pRec
0.192

Intolerance Scores

loftool
0.140
rvis_EVS
-0.86
rvis_percentile_EVS
10.89

Haploinsufficiency Scores

pHI
0.291
hipred
N
hipred_score
0.348
ghis
0.497

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.169

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Slc5a2
Phenotype
adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; digestive/alimentary phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; skeleton phenotype; immune system phenotype;

Gene ontology

Biological process
carbohydrate metabolic process;sodium ion transport;hexose transmembrane transport;glucose transmembrane transport
Cellular component
plasma membrane;integral component of membrane;extracellular exosome
Molecular function
low-affinity glucose:sodium symporter activity;glucose:sodium symporter activity