SLC2A2

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

Basic information

Region (hg38): 3:170996347-171026743

Previous symbols: [ "GLUT2" ]

Links

ENSG00000163581 ∙ NCBI:6514 ∙ OMIM:138160 ∙ HGNC:11006 ∙ Uniprot:P11168 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• glycogen storage disease due to GLUT2 deficiency (Definitive), mode of inheritance: AR
• glycogen storage disease due to GLUT2 deficiency (Strong), mode of inheritance: AR
• neonatal diabetes mellitus (Strong), mode of inheritance: AR
• transient neonatal diabetes mellitus (Strong), mode of inheritance: AR
• permanent neonatal diabetes mellitus (Strong), mode of inheritance: AR
• glycogen storage disease due to GLUT2 deficiency (Strong), mode of inheritance: AR
• glycogen storage disease due to GLUT2 deficiency (Supportive), mode of inheritance: AR
• glycogen storage disease due to GLUT2 deficiency (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Fanconi-Bickel syndrome; Glycogen storage disease XI; Neonatal diabetes mellitus	AR	Biochemical; Endocrine	Dietary measures (eg, frequent feeds, cornstarch) can be beneficial; In mildly affected individuals, dietary measures (eg, free glucose and galactose restriction) may be beneficial in terms of growth; Individuals may also manifest with neonatal diabetes mellitus, and awareness may allow preventive measures and prompt treatment related to severe episodes	Biochemical; Endocrine; Gastrointestinal; Renal	15397919; 6274135; 3153325; 8362811; 7632512; 7564233; 9266402; 9354798; 10987651; 11044475; 11810292; 19480329; 21271664; 22145468; 22350464; 22214819; 22060631; 22831748; 22660720

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC2A2 gene.

• Fanconi-Bickel syndrome (22 variants)
• Type 2 diabetes mellitus (2 variants)
• Fanconi-Bickel syndrome;Type 2 diabetes mellitus (2 variants)
• SLC2A2-related disorder (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC2A2 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			2	36	1	39
missense	1	4	78	3	3	89
nonsense	8	1				9
start loss	1					1
frameshift	8	4				12
inframe indel			3			3
splice donor/acceptor (+/-2bp)	4	3	1			8
splice region		1	4	11	2	18
non coding			26	28	33	87
Total	22	12	110	67	37

Highest pathogenic variant AF is 0.0000723

Variants in SLC2A2

This is a list of pathogenic ClinVar variants found in the SLC2A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-170996372-T-C		Fanconi-Bickel syndrome	Uncertain significance (Jan 13, 2018)
3-170996483-A-G		Fanconi-Bickel syndrome	Uncertain significance (Jan 12, 2018)
3-170996554-G-A		Fanconi-Bickel syndrome	Benign (Jan 13, 2018)
3-170996600-A-G		Fanconi-Bickel syndrome	Uncertain significance (Jan 13, 2018)
3-170996643-T-C		Fanconi-Bickel syndrome	Likely benign (Jan 13, 2018)
3-170996646-G-A		Fanconi-Bickel syndrome	Benign (Jan 13, 2018)
3-170996681-A-T		Fanconi-Bickel syndrome	Benign (Jan 13, 2018)
3-170996696-C-T		Fanconi-Bickel syndrome	Uncertain significance (Jan 13, 2018)
3-170996702-A-G		Fanconi-Bickel syndrome	Uncertain significance (Jan 12, 2018)
3-170996739-A-G		Fanconi-Bickel syndrome	Uncertain significance (Jan 12, 2018)
3-170996817-C-T		Fanconi-Bickel syndrome	Uncertain significance (Jan 12, 2018)
3-170996843-TA-T		Fanconi-Bickel syndrome	Likely benign (Jun 14, 2016)
3-170996899-C-T		Fanconi-Bickel syndrome	Uncertain significance (Jan 13, 2018)
3-170996943-A-C		Fanconi-Bickel syndrome	Uncertain significance (Jan 13, 2018)
3-170996968-CCTTTA-C		Fanconi-Bickel syndrome	Likely benign (Jun 14, 2016)
3-170996983-T-G		Fanconi-Bickel syndrome	Benign (Jan 13, 2018)
3-170996994-G-A		Fanconi-Bickel syndrome	Benign (Jan 12, 2018)
3-170997107-A-G		Fanconi-Bickel syndrome	Uncertain significance (Jan 13, 2018)
3-170997177-A-G		Fanconi-Bickel syndrome	Uncertain significance (Jan 12, 2018)
3-170997178-C-G		Fanconi-Bickel syndrome	Benign (Jan 12, 2018)
3-170997205-A-T		Fanconi-Bickel syndrome	Uncertain significance (Jan 13, 2018)
3-170997295-AC-A		Fanconi-Bickel syndrome	Uncertain significance (Jun 14, 2016)
3-170997335-T-A		Fanconi-Bickel syndrome	Uncertain significance (Jan 12, 2018)
3-170997417-A-G		Fanconi-Bickel syndrome	Likely benign (Jan 13, 2018)
3-170997427-A-G		Fanconi-Bickel syndrome	Benign (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC2A2	protein_coding	protein_coding	ENST00000314251	11	30403

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.43e-8	0.934	125696	0	52	125748	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.936	227	270	0.840	0.0000134	3393
Missense in Polyphen		87	106.8	0.81461		1398
Synonymous	0.104	96	97.3	0.987	0.00000492	1061
Loss of Function	1.87	16	26.3	0.608	0.00000157	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000784	0.000720
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.000272	0.000272
South Asian	0.000137	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Facilitative glucose transporter. This isoform likely mediates the bidirectional transfer of glucose across the plasma membrane of hepatocytes and is responsible for uptake of glucose by the beta cells; may comprise part of the glucose-sensing mechanism of the beta cell. May also participate with the Na(+)/glucose cotransporter in the transcellular transport of glucose in the small intestine and kidney.
• Disease: DISEASE: Fanconi-Bickel syndrome (FBS) [MIM:227810]: Rare, well- defined clinical entity, inherited in an autosomal recessive mode and characterized by hepatorenal glycogen accumulation, proximal renal tubular dysfunction, and impaired utilization of glucose and galactose. {ECO:0000269|PubMed:10987651, ECO:0000269|PubMed:11044475}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Central carbon metabolism in cancer - Homo sapiens (human);Type II diabetes mellitus - Homo sapiens (human);Insulin resistance - Homo sapiens (human);Carbohydrate digestion and absorption - Homo sapiens (human);Maturity onset diabetes of the young - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Prolactin signaling pathway - Homo sapiens (human);Insulin secretion - Homo sapiens (human);Anti-diabetic Drug Potassium Channel Inhibitors Pathway, Pharmacodynamics;Warburg Effect;Glycolysis;Glibenclamide Action Pathway;Gliclazide Action Pathway;Trehalose Degradation;Glycogenosis, Type VII. Tarui disease;Gluconeogenesis;Glucose-Alanine Cycle;Glycogenosis, Type IA. Von gierke disease;Glycogenosis, Type IC;Fanconi-bickel syndrome;Glycogen Storage Disease Type 1A (GSD1A) or Von Gierke Disease;Triosephosphate isomerase;Fructose-1,6-diphosphatase deficiency;Phosphoenolpyruvate carboxykinase deficiency 1 (PEPCK1);Pancreas Function;Lactose Degradation;Repaglinide Action Pathway;Nateglinide Action Pathway;Lactose Intolerance;Glycogenosis, Type IB;Type II diabetes mellitus;Cori Cycle;Nuclear Receptors Meta-Pathway;NRF2 pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Glycolysis and Gluconeogenesis;Metabolism;SLC-mediated transmembrane transport;Transport of small molecules;Regulation of insulin secretion;Aminosugars metabolism;Fructose and mannose metabolism;Galactose metabolism;Cellular hexose transport;Intestinal hexose absorption;Intestinal absorption;Digestion and absorption;Integration of energy metabolism;FOXA2 and FOXA3 transcription factor networks (Consensus)

Recessive Scores

• pRec: 0.731

Intolerance Scores

• loftool: 0.471
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.43

Haploinsufficiency Scores

• pHI: 0.543
• hipred: N
• hipred_score: 0.307
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.736

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Slc2a2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype

Zebrafish Information Network

• Gene name: slc2a2
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: dead

Gene ontology

• Biological process: carbohydrate metabolic process;hexose transmembrane transport;regulation of insulin secretion;dehydroascorbic acid transport;intestinal hexose absorption;glucose transmembrane transport
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane;brush border;cell-cell junction;membrane;apical plasma membrane
• Molecular function: glucose transmembrane transporter activity;hexose transmembrane transporter activity;dehydroascorbic acid transmembrane transporter activity;D-glucose transmembrane transporter activity