SLC2A4
solute carrier family 2 member 4, the group of Solute carrier family 2
Basic information
Region (hg38): 17:7281718-7288257
Previous symbols: [ "GLUT4" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC2A4 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 | 1 | |||||
| missense | 21 | 25 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 21 | 4 | 1 |
Variants in SLC2A4
This is a list of pathogenic ClinVar variants found in the SLC2A4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-7281958-A-G | not specified | Uncertain significance (Dec 17, 2021) | ||
| 17-7283474-T-C | not specified | Uncertain significance (May 30, 2024) | ||
| 17-7283522-A-C | not specified | Uncertain significance (May 07, 2024) | ||
| 17-7283546-G-A | not specified | Uncertain significance (Feb 27, 2023) | ||
| 17-7283558-C-G | Likely benign (Nov 01, 2022) | |||
| 17-7283770-C-T | not specified | Uncertain significance (Dec 14, 2022) | ||
| 17-7283865-A-T | Likely benign (Jul 06, 2018) | |||
| 17-7284015-G-A | not specified | Uncertain significance (Jul 13, 2021) | ||
| 17-7284036-G-A | not specified | Uncertain significance (Apr 23, 2024) | ||
| 17-7284083-C-T | Benign (May 15, 2018) | |||
| 17-7284228-G-C | not specified | Uncertain significance (Apr 25, 2022) | ||
| 17-7284334-C-T | not specified | Uncertain significance (Feb 28, 2023) | ||
| 17-7284352-C-G | not specified | Uncertain significance (May 03, 2023) | ||
| 17-7284361-G-A | not specified | Uncertain significance (Mar 07, 2024) | ||
| 17-7284562-C-T | not specified | Uncertain significance (Jan 04, 2022) | ||
| 17-7284602-G-A | not specified | Likely benign (Sep 26, 2022) | ||
| 17-7284610-C-T | not specified | Uncertain significance (Nov 10, 2022) | ||
| 17-7284911-T-C | not specified | Uncertain significance (Dec 16, 2023) | ||
| 17-7285091-T-G | not specified | Uncertain significance (Dec 19, 2023) | ||
| 17-7285103-C-T | not specified | Uncertain significance (Jun 10, 2022) | ||
| 17-7285107-C-T | not specified | Uncertain significance (Feb 26, 2024) | ||
| 17-7285119-C-T | not specified | Uncertain significance (Jul 09, 2021) | ||
| 17-7285140-C-T | Likely benign (Jul 01, 2024) | |||
| 17-7285167-T-A | not specified | Uncertain significance (Jun 07, 2023) | ||
| 17-7285709-G-A | not specified | Uncertain significance (Oct 02, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC2A4 | protein_coding | protein_coding | ENST00000317370 | 11 | 6591 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000471 | 0.993 | 125729 | 0 | 19 | 125748 | 0.0000756 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.638 | 259 | 290 | 0.894 | 0.0000189 | 3198 |
| Missense in Polyphen | 85 | 104.38 | 0.81433 | 1126 | ||
| Synonymous | -1.29 | 146 | 127 | 1.15 | 0.00000857 | 1145 |
| Loss of Function | 2.38 | 11 | 23.4 | 0.469 | 0.00000128 | 244 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000269 | 0.000268 |
| Ashkenazi Jewish | 0.000199 | 0.000198 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000537 | 0.0000527 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000655 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Insulin-regulated facilitative glucose transporter.;
- Disease
- DISEASE: Diabetes mellitus, non-insulin-dependent (NIDDM) [MIM:125853]: A multifactorial disorder of glucose homeostasis caused by a lack of sensitivity to the body's own insulin. Affected individuals usually have an obese body habitus and manifestations of a metabolic syndrome characterized by diabetes, insulin resistance, hypertension and hypertriglyceridemia. The disease results in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269|PubMed:1521731, ECO:0000269|PubMed:1756912, ECO:0000269|PubMed:1918382}. Note=The disease may be caused by mutations affecting the gene represented in this entry.;
- Pathway
- Adipocytokine signaling pathway - Homo sapiens (human);Type II diabetes mellitus - Homo sapiens (human);Insulin resistance - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Metformin Pathway, Pharmacodynamic;Glucose-Alanine Cycle;Insulin Signalling;AMP-activated Protein Kinase (AMPK) Signaling;Type II diabetes mellitus;Cori Cycle;Transcriptional regulation of white adipocyte differentiation;Adipogenesis;Vitamin D Receptor Pathway;Nuclear Receptors Meta-Pathway;NRF2 pathway;Transcription factor regulation in adipogenesis;Angiopoietin Like Protein 8 Regulatory Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;SCFA and skeletal muscle substrate metabolism;Insulin Signaling;Glycolysis and Gluconeogenesis;SLC-mediated transmembrane transport;Transport of small molecules;Aminosugars metabolism;Fructose and mannose metabolism;Galactose metabolism;Vitamin C metabolism;Cellular hexose transport;Arf6 trafficking events;Leptin;Insulin-mediated glucose transport;Class I PI3K signaling events mediated by Akt
(Consensus)
Recessive Scores
- pRec
- 0.140
Intolerance Scores
- loftool
- 0.304
- rvis_EVS
- -0.18
- rvis_percentile_EVS
- 40.45
Haploinsufficiency Scores
- pHI
- 0.329
- hipred
- Y
- hipred_score
- 0.638
- ghis
- 0.546
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.594
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc2a4
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); liver/biliary system phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary 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);
Gene ontology
- Biological process
- carbohydrate metabolic process;amylopectin biosynthetic process;cellular response to insulin stimulus;glucose homeostasis;glucose import in response to insulin stimulus;response to ethanol;glucose import;brown fat cell differentiation;cellular response to tumor necrosis factor;cellular response to hypoxia;cellular response to osmotic stress;regulation of synaptic vesicle budding from presynaptic endocytic zone membrane;glucose transmembrane transport
- Cellular component
- multivesicular body;cytosol;plasma membrane;integral component of plasma membrane;clathrin-coated pit;external side of plasma membrane;endomembrane system;vesicle membrane;membrane;sarcoplasmic reticulum;clathrin-coated vesicle;trans-Golgi network transport vesicle;T-tubule;cytoplasmic vesicle membrane;insulin-responsive compartment;membrane raft;perinuclear region of cytoplasm;extracellular exosome;presynapse
- Molecular function
- glucose transmembrane transporter activity;protein binding;D-glucose transmembrane transporter activity