SLC5A2
Basic information
Region (hg38): 16:31483002-31490860
Previous symbols: [ "SGLT2" ]
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Renal glucosuria | AD/AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Renal | 12436245; 21165652 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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 | 18 | ||||
missense | 95 | 101 | ||||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 8 | |||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 1 | 6 | 5 | 12 | ||
non coding | 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) | ||
16-31483155-G-A | Familial renal glucosuria | Uncertain significance (Jan 13, 2018) | ||
16-31483162-C-T | Familial renal glucosuria | Uncertain significance (Jan 12, 2018) | ||
16-31483188-G-C | Inborn genetic diseases | Uncertain significance (Dec 03, 2021) | ||
16-31483196-T-C | Familial renal glucosuria | Benign (Dec 31, 2019) | ||
16-31483222-T-C | Inborn genetic diseases | Uncertain significance (Mar 21, 2024) | ||
16-31484350-G-C | Benign (Nov 12, 2018) | |||
16-31484655-C-G | SLC5A2-related disorder | Likely benign (Apr 25, 2019) | ||
16-31484657-C-A | Familial renal glucosuria | Pathogenic (Mar 01, 2011) | ||
16-31484698-C-T | Familial renal glucosuria | Uncertain significance (Jan 12, 2018) | ||
16-31484709-T-C | SLC5A2-related disorder | Uncertain significance (May 01, 2023) | ||
16-31484717-GGCAGGACGCA-G | Uncertain significance (Sep 16, 2018) | |||
16-31484724-C-T | SLC5A2-related disorder | Uncertain significance (Feb 10, 2024) | ||
16-31484731-TG-T | Uncertain significance (Sep 16, 2018) | |||
16-31484736-T-G | Uncertain significance (Mar 10, 2023) | |||
16-31484743-C-T | Familial renal glucosuria | Uncertain significance (Nov 08, 2021) | ||
16-31484846-A-G | Familial renal glucosuria | Uncertain significance (Apr 29, 2022) | ||
16-31484847-T-A | Familial renal glucosuria | Uncertain significance (Aug 15, 2019) | ||
16-31484874-C-A | Inborn genetic diseases | Uncertain significance (Feb 22, 2023) | ||
16-31484885-G-A | Familial renal glucosuria | Pathogenic (Aug 02, 2016) | ||
16-31484914-C-A | Familial renal glucosuria | Pathogenic (Mar 01, 2011) | ||
16-31484915-G-C | Uncertain significance (May 28, 2021) | |||
16-31484914-C-CTT | Familial renal glucosuria | Likely pathogenic (Jun 20, 2019) | ||
16-31485730-C-T | Familial renal glucosuria | Uncertain significance (Apr 04, 2024) | ||
16-31485731-G-A | SLC5A2-related disorder | Likely benign (Jan 17, 2020) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SLC5A2 | protein_coding | protein_coding | ENST00000330498 | 14 | 7859 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.92e-14 | 0.179 | 125639 | 0 | 109 | 125748 | 0.000434 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -1.16 | 472 | 406 | 1.16 | 0.0000258 | 4262 |
Missense in Polyphen | 208 | 197.17 | 1.0549 | 2064 | ||
Synonymous | -2.18 | 218 | 181 | 1.21 | 0.0000126 | 1440 |
Loss of Function | 1.02 | 24 | 30.0 | 0.799 | 0.00000143 | 323 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00122 | 0.00122 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.000147 | 0.000139 |
European (Non-Finnish) | 0.000583 | 0.000571 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.000294 | 0.000294 |
Other | 0.00114 | 0.00114 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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