SLC2A13

solute carrier family 2 member 13, the group of Solute carrier family 2

Basic information

Region (hg38): 12:39755024-40106089

Links

ENSG00000151229 ∙ NCBI:114134 ∙ OMIM:611036 ∙ HGNC:15956 ∙ Uniprot:Q96QE2 ∙ 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 SLC2A13 gene.

• Inborn genetic diseases (23 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC2A13 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						0
missense			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in SLC2A13

This is a list of pathogenic ClinVar variants found in the SLC2A13 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-39760097-A-G		not specified	Uncertain significance (Dec 11, 2023)
12-39760234-G-A		not specified	Uncertain significance (Sep 27, 2022)
12-39764499-G-C		not specified	Uncertain significance (Dec 16, 2023)
12-39764544-C-A		not specified	Uncertain significance (Jan 23, 2024)
12-39764567-A-C		not specified	Uncertain significance (Jan 04, 2022)
12-39764815-C-T		not specified	Uncertain significance (Jun 21, 2021)
12-39830124-G-A		not specified	Uncertain significance (Feb 27, 2024)
12-39830176-T-C		not specified	Uncertain significance (Mar 04, 2024)
12-39864777-G-A		not specified	Uncertain significance (Jan 09, 2024)
12-39864819-C-T		not specified	Uncertain significance (Nov 15, 2023)
12-39951309-C-A		not specified	Uncertain significance (May 15, 2023)
12-39951323-C-A		not specified	Uncertain significance (Dec 16, 2023)
12-39951359-G-T		not specified	Uncertain significance (Sep 22, 2022)
12-40028449-C-A		not specified	Uncertain significance (Aug 10, 2021)
12-40028480-G-C		not specified	Uncertain significance (Jan 04, 2022)
12-40048072-T-C		not specified	Uncertain significance (Jun 09, 2022)
12-40048081-G-C		not specified	Uncertain significance (Nov 17, 2022)
12-40048118-T-G		not specified	Uncertain significance (Jun 16, 2023)
12-40048181-T-C		not specified	Uncertain significance (Jan 26, 2023)
12-40105296-C-G		not specified	Uncertain significance (Jul 11, 2023)
12-40105321-G-A		not specified	Uncertain significance (May 05, 2023)
12-40105337-A-G		not specified	Uncertain significance (Feb 17, 2022)
12-40105390-G-A		not specified	Uncertain significance (Dec 28, 2022)
12-40105445-G-C		not specified	Uncertain significance (Jul 17, 2023)
12-40105472-G-A		not specified	Uncertain significance (Jun 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC2A13	protein_coding	protein_coding	ENST00000280871	10	351069

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.833	0.167	125698	0	7	125705	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.48	249	324	0.768	0.0000159	4121
Missense in Polyphen		64	122.96	0.52048		1424
Synonymous	-0.809	134	123	1.09	0.00000619	1331
Loss of Function	4.02	5	27.9	0.179	0.00000142	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.000117	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.000117	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: H(+)-myo-inositol cotransporter. Can also transport related stereoisomers. {ECO:0000269|PubMed:11500374}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Inositol transporters;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Phosphatidylinositol phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.190

Intolerance Scores

• loftool: 0.0343
• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• pHI: 0.268
• hipred: Y
• hipred_score: 0.664
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.119

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc2a13

Zebrafish Information Network

• Gene name: slc2a13b
• Affected structure: vH ionocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased functionality

Gene ontology

• Biological process: myo-inositol transport;transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: myo-inositol:proton symporter activity