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

ENSG00000140675 ∙ NCBI:6524 ∙ OMIM:182381 ∙ HGNC:11037 ∙ Uniprot:P31639 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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
• familial renal glucosuria (Definitive), mode of inheritance: AR
• familial renal glucosuria (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the SLC5A2 gene.

• Familial renal glucosuria (3 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			19	3	2	24
missense		7	195		1	203
nonsense	1	4				5
start loss			1			1
frameshift	1	8				9
inframe indel			4			4
splice donor/acceptor (+/-2bp)	1	5	1			7
splice region		1	10	1		12
non coding			9	3	3	15
Total	3	24	229	6	6

Highest pathogenic variant AF is 0.0000131

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
16-31483138-T-C		Familial renal glucosuria	Uncertain significance (Mar 04, 2024)
16-31483140-G-A		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)
16-31483153-A-T		Familial renal glucosuria	Uncertain significance (Apr 20, 2024)
16-31483155-G-A		Familial renal glucosuria	Uncertain significance (Jan 13, 2018)
16-31483162-C-T		Familial renal glucosuria	Uncertain significance (May 15, 2024)
16-31483183-A-G		Familial renal glucosuria	Uncertain significance (Apr 07, 2024)
16-31483188-G-C		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)
16-31483196-T-C		Familial renal glucosuria	Benign (Dec 31, 2019)
16-31483203-C-A		Familial renal glucosuria	Uncertain significance (May 16, 2024)
16-31483213-T-A		Inborn genetic diseases	Uncertain significance (Oct 12, 2024)
16-31483222-T-C		Inborn genetic diseases	Uncertain significance (Mar 21, 2024)
16-31483239-C-G		Inborn genetic diseases • Familial renal glucosuria	Uncertain significance (Sep 30, 2024)
16-31483251-G-A		Familial renal glucosuria	Uncertain significance (Dec 27, 2023)
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)
16-31484704-G-A		Familial renal glucosuria	Uncertain significance (May 10, 2024)
16-31484709-T-C		SLC5A2-related disorder	Uncertain significance (May 01, 2023)
16-31484710-A-C		Familial renal glucosuria	Uncertain significance (Feb 12, 2024)
16-31484713-T-G		Familial renal glucosuria	Uncertain significance (Jan 23, 2024)
16-31484717-GGCAGGACGCA-G			Uncertain significance (Sep 16, 2018)
16-31484724-C-T		SLC5A2-related disorder • Familial renal glucosuria	Uncertain significance (Jul 26, 2024)
16-31484731-TG-T			Uncertain significance (Sep 16, 2018)
16-31484736-T-C		Inborn genetic diseases • Familial renal glucosuria	Uncertain significance (Nov 25, 2024)

GnomAD

Source: gnomAD

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: 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

	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