SLC2A10

solute carrier family 2 member 10, the group of Solute carrier family 2

Basic information

Region (hg38): 20:46709648-46736347

Links

ENSG00000197496 ∙ NCBI:81031 ∙ OMIM:606145 ∙ HGNC:13444 ∙ Uniprot:O95528 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• arterial tortuosity syndrome (Definitive), mode of inheritance: AR
• arterial tortuosity syndrome (Strong), mode of inheritance: AR
• arterial tortuosity syndrome (Supportive), mode of inheritance: AR
• arterial tortuosity syndrome (Definitive), mode of inheritance: AR
• arterial tortuosity syndrome (Strong), mode of inheritance: AR
• familial thoracic aortic aneurysm and aortic dissection (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Arterial tortuosity syndrome	AR	Cardiovascular	Individuals appear to be at increased risk of cradiovascular manifestations, such as ischemic events, arterial aneurysm, and other findings, and preventive measures and prompt treatment may be beneficial	Cardiovascular; Dermatologic; Genitourinary; Musculoskeletal; Renal	6033167; 12801113; 16550171; 17935213; 18565096; 19508422; 19781076; 29323665

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC2A10 gene.

• Arterial tortuosity syndrome (420 variants)
• Familial thoracic aortic aneurysm and aortic dissection (198 variants)
• not provided (160 variants)
• not specified (80 variants)
• Cardiovascular phenotype (7 variants)
• Inborn genetic diseases (5 variants)
• SLC2A10-related condition (5 variants)
• Ehlers-Danlos syndrome, classic type (1 variants)
• Aortic aneurysm, familial thoracic 6 (1 variants)
• Bicuspid aortic valve (1 variants)
• Aortic aneurysm, familial thoracic 2 (1 variants)
• Familial thoracic aortic aneurysm and aortic dissection;Disproportionate tall stature (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC2A10 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	125		126
missense	1	7	216	8	4	236
nonsense	3	4				7
start loss	1					1
frameshift	5	5	1			11
inframe indel	1		1			2
splice donor/acceptor (+/-2bp)		4	1			5
splice region			4	3		7
non coding			43	42	29	114
Total	11	20	263	175	33

Highest pathogenic variant AF is 0.000118

Variants in SLC2A10

This is a list of pathogenic ClinVar variants found in the SLC2A10 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-46709677-G-T		Arterial tortuosity syndrome	Uncertain significance (Jan 13, 2018)
20-46709682-G-T		Arterial tortuosity syndrome	Uncertain significance (Jan 13, 2018)
20-46709706-G-GC		not specified	Likely benign (Apr 03, 2017)
20-46709710-C-T		not specified • Arterial tortuosity syndrome	Benign (Jan 12, 2018)
20-46709715-A-G		Arterial tortuosity syndrome	Conflicting classifications of pathogenicity (Jan 13, 2018)
20-46709722-C-T		not specified • Arterial tortuosity syndrome • Familial thoracic aortic aneurysm and aortic dissection	Conflicting classifications of pathogenicity (Mar 01, 2023)
20-46709727-C-G		SLC2A10-related disorder	Likely benign (Jun 29, 2022)
20-46709737-A-G		Arterial tortuosity syndrome	Conflicting classifications of pathogenicity (Mar 26, 2024)
20-46709740-G-A		Arterial tortuosity syndrome	Uncertain significance (May 27, 2022)
20-46709746-T-A		Familial thoracic aortic aneurysm and aortic dissection	Uncertain significance (Jun 30, 2021)
20-46709749-C-G		not specified • Arterial tortuosity syndrome	Likely benign (Jul 22, 2023)
20-46709750-G-A		Arterial tortuosity syndrome	Likely benign (Sep 09, 2023)
20-46709754-G-C		Arterial tortuosity syndrome	Likely benign (Dec 23, 2022)
20-46709754-G-T		Arterial tortuosity syndrome	Likely benign (Jan 29, 2022)
20-46709968-C-T			Likely benign (Aug 03, 2018)
20-46724806-AGGAT-A			Benign (Aug 06, 2019)
20-46724806-A-AGGAT			Benign (Nov 14, 2019)
20-46724875-C-CGGACGGAT			Likely benign (Sep 21, 2019)
20-46724875-C-CGGATGGAT			Benign (Nov 14, 2019)
20-46724875-C-CGGATGGATGGATGGAT			Benign (Aug 10, 2019)
20-46724875-C-CGGATGGATGGAT			Benign (Nov 14, 2019)
20-46724905-GTTTGA-G			Likely benign (Aug 06, 2019)
20-46724918-G-GT			Likely benign (Jun 14, 2018)
20-46724925-A-G			Likely benign (Jun 14, 2018)
20-46725023-C-T		Arterial tortuosity syndrome	Likely benign (Sep 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC2A10	protein_coding	protein_coding	ENST00000359271	5	26840

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.57e-8	0.225	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.755	338	301	1.12	0.0000191	3399
Missense in Polyphen		115	112.48	1.0224		1316
Synonymous	-1.53	162	139	1.17	0.00000886	1295
Loss of Function	0.435	13	14.8	0.878	8.37e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000608	0.000608
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000282	0.000281
Middle Eastern	0.000163	0.000163
South Asian	0.000163	0.000163
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Facilitative glucose transporter.
• 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: 0.180

Intolerance Scores

• loftool: 0.217
• rvis_EVS: 0.23
• rvis_percentile_EVS: 68.52

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.291
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.561

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc2a10
• Phenotype: renal/urinary system phenotype; immune system phenotype; respiratory system phenotype; 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); hematopoietic system phenotype

Zebrafish Information Network

• Gene name: slc2a10
• Affected structure: vasculature
• Phenotype tag: abnormal
• Phenotype quality: irregular spatial pattern

Gene ontology

• Biological process: hexose transmembrane transport;proton transmembrane transport;glucose transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;endomembrane system;integral component of membrane;perinuclear region of cytoplasm
• Molecular function: carbohydrate:proton symporter activity;D-glucose transmembrane transporter activity