SLC2A4

solute carrier family 2 member 4, the group of Solute carrier family 2

Basic information

Region (hg38): 17:7281717-7288257

Previous symbols: [ "GLUT4" ]

Links

ENSG00000181856 ∙ NCBI:6517 ∙ OMIM:138190 ∙ HGNC:11009 ∙ Uniprot:P14672 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC2A4 gene.

• Inborn genetic diseases (16 variants)
• not provided (5 variants)
• Type 2 diabetes mellitus (1 variants)

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	1
missense			15	4		19
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	15	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)
17-7283546-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)
17-7284083-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 (Jun 01, 2022)
17-7285167-T-A		not specified	Uncertain significance (Jun 07, 2023)
17-7285709-G-A		not specified	Uncertain significance (Oct 02, 2023)
17-7285729-G-A		Type 2 diabetes mellitus	Likely benign (Nov 01, 2022)
17-7285746-C-G		not specified	Uncertain significance (Jul 20, 2021)
17-7285807-G-A		not specified	Uncertain significance (Apr 26, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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