Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	64849
Gene name	Solute carrier family 13 member 3
Gene symbol	SLC13A3
Synonyms (NCBI Gene)	ARLIAKNADC3NaC3SDCT2
Chromosome	20
Chromosome location	20q13.12
Summary	Mammalian sodium-dicarboxylate cotransporters transport succinate and other Krebs cycle intermediates. They fall into 2 categories based on their substrate affinity: low affinity and high affinity. Both the low- and high-affinity transporters play an impo

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs199961976	T>C	Pathogenic	Intron variant
rs1568904872	C>T	Pathogenic	Coding sequence variant, missense variant
rs1568927501	G>T	Pathogenic	Coding sequence variant, missense variant

Show/Hide all (91)

miRTarBase ID	miRNA	Experiments
MIRT1352473	hsa-miR-1275	CLIP-seq
MIRT1352474	hsa-miR-150	CLIP-seq
MIRT1352475	hsa-miR-3173-3p	CLIP-seq
MIRT1352476	hsa-miR-34b	CLIP-seq
MIRT1352477	hsa-miR-412	CLIP-seq
MIRT1352478	hsa-miR-4257	CLIP-seq
MIRT1352479	hsa-miR-4420	CLIP-seq
MIRT1352480	hsa-miR-4428	CLIP-seq
MIRT1352481	hsa-miR-4477a	CLIP-seq
MIRT1352482	hsa-miR-4477b	CLIP-seq
MIRT1352483	hsa-miR-4488	CLIP-seq
MIRT1352484	hsa-miR-4512	CLIP-seq
MIRT1352485	hsa-miR-4525	CLIP-seq
MIRT1352486	hsa-miR-4665-5p	CLIP-seq
MIRT1352487	hsa-miR-4697-5p	CLIP-seq
MIRT1352488	hsa-miR-4713-5p	CLIP-seq
MIRT1352489	hsa-miR-4723-5p	CLIP-seq
MIRT1352490	hsa-miR-4757-5p	CLIP-seq
MIRT1352491	hsa-miR-532-3p	CLIP-seq
MIRT1352492	hsa-miR-539	CLIP-seq
MIRT1352493	hsa-miR-548a-5p	CLIP-seq
MIRT1352494	hsa-miR-548ab	CLIP-seq
MIRT1352495	hsa-miR-548ak	CLIP-seq
MIRT1352496	hsa-miR-548b-5p	CLIP-seq
MIRT1352497	hsa-miR-548c-5p	CLIP-seq
MIRT1352498	hsa-miR-548d-5p	CLIP-seq
MIRT1352499	hsa-miR-548h	CLIP-seq
MIRT1352500	hsa-miR-548i	CLIP-seq
MIRT1352501	hsa-miR-548j	CLIP-seq
MIRT1352502	hsa-miR-548w	CLIP-seq
MIRT1352503	hsa-miR-548y	CLIP-seq
MIRT1352504	hsa-miR-559	CLIP-seq
MIRT1352505	hsa-miR-625	CLIP-seq
MIRT1352506	hsa-miR-637	CLIP-seq
MIRT1352507	hsa-miR-676	CLIP-seq
MIRT2328800	hsa-miR-128	CLIP-seq
MIRT2328801	hsa-miR-1301	CLIP-seq
MIRT1352474	hsa-miR-150	CLIP-seq
MIRT2328802	hsa-miR-15a	CLIP-seq
MIRT2328803	hsa-miR-15b	CLIP-seq
MIRT2328804	hsa-miR-16	CLIP-seq
MIRT2328805	hsa-miR-195	CLIP-seq
MIRT2328806	hsa-miR-27a	CLIP-seq
MIRT2328807	hsa-miR-27b	CLIP-seq
MIRT2328808	hsa-miR-3156-3p	CLIP-seq
MIRT2328809	hsa-miR-3189-3p	CLIP-seq
MIRT2328810	hsa-miR-424	CLIP-seq
MIRT1352478	hsa-miR-4257	CLIP-seq
MIRT2328811	hsa-miR-4301	CLIP-seq
MIRT2328812	hsa-miR-4468	CLIP-seq
MIRT1352484	hsa-miR-4512	CLIP-seq
MIRT2328813	hsa-miR-4691-3p	CLIP-seq
MIRT1352488	hsa-miR-4713-5p	CLIP-seq
MIRT2328814	hsa-miR-497	CLIP-seq
MIRT2328815	hsa-miR-498	CLIP-seq
MIRT2328816	hsa-miR-5047	CLIP-seq
MIRT2328817	hsa-miR-507	CLIP-seq
MIRT2328818	hsa-miR-513a-5p	CLIP-seq
MIRT1352491	hsa-miR-532-3p	CLIP-seq
MIRT2328819	hsa-miR-543	CLIP-seq
MIRT2328820	hsa-miR-545	CLIP-seq
MIRT2328821	hsa-miR-557	CLIP-seq
MIRT2328801	hsa-miR-1301	CLIP-seq
MIRT1352475	hsa-miR-3173-3p	CLIP-seq
MIRT2459475	hsa-miR-3609	CLIP-seq
MIRT2459476	hsa-miR-3614-5p	CLIP-seq
MIRT2459477	hsa-miR-3670	CLIP-seq
MIRT2459478	hsa-miR-3689d	CLIP-seq
MIRT2459479	hsa-miR-3978	CLIP-seq
MIRT2459480	hsa-miR-4633-3p	CLIP-seq
MIRT2459481	hsa-miR-4690-3p	CLIP-seq
MIRT2328816	hsa-miR-5047	CLIP-seq
MIRT2459482	hsa-miR-548ah	CLIP-seq
MIRT2459483	hsa-miR-890	CLIP-seq
MIRT2459477	hsa-miR-3670	CLIP-seq
MIRT2690866	hsa-miR-1200	CLIP-seq
MIRT2690867	hsa-miR-1207-3p	CLIP-seq
MIRT2328801	hsa-miR-1301	CLIP-seq
MIRT2690868	hsa-miR-2861	CLIP-seq
MIRT2690869	hsa-miR-3178	CLIP-seq
MIRT2690870	hsa-miR-3616-3p	CLIP-seq
MIRT2459477	hsa-miR-3670	CLIP-seq
MIRT2690871	hsa-miR-3944-5p	CLIP-seq
MIRT2690872	hsa-miR-4297	CLIP-seq
MIRT2690873	hsa-miR-4324	CLIP-seq
MIRT2690874	hsa-miR-4486	CLIP-seq
MIRT1352484	hsa-miR-4512	CLIP-seq
MIRT2690875	hsa-miR-4660	CLIP-seq
MIRT2690876	hsa-miR-4721	CLIP-seq
MIRT2328816	hsa-miR-5047	CLIP-seq
MIRT2690877	hsa-miR-544b	CLIP-seq

Show/Hide all (1)

Transcription factor	Regulation	Reference
PITX2	Unknown	21873665

Show/Hide all (43)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005310	Function	Dicarboxylic acid transmembrane transporter activity	IDA	10992006
GO:0005310	Function	Dicarboxylic acid transmembrane transporter activity	TAS	10992006
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006814	Process	Sodium ion transport	IEA
GO:0006835	Process	Dicarboxylic acid transport	IDA	10992006
GO:0006835	Process	Dicarboxylic acid transport	IEA
GO:0006835	Process	Dicarboxylic acid transport	TAS	10992006
GO:0006869	Process	Lipid transport	IEA
GO:0015137	Function	Citrate transmembrane transporter activity	IBA
GO:0015137	Function	Citrate transmembrane transporter activity	ISS
GO:0015139	Function	Alpha-ketoglutarate transmembrane transporter activity	IDA	30635937
GO:0015141	Function	Succinate transmembrane transporter activity	IBA
GO:0015141	Function	Succinate transmembrane transporter activity	IDA	10992006, 21264516, 24247155, 26176240, 30635937
GO:0015141	Function	Succinate transmembrane transporter activity	IEA
GO:0015141	Function	Succinate transmembrane transporter activity	TAS	10992006
GO:0015293	Function	Symporter activity	IEA
GO:0015362	Function	High-affinity sodium:dicarboxylate symporter activity	IEA
GO:0015362	Function	High-affinity sodium:dicarboxylate symporter activity	TAS
GO:0015370	Function	Solute:sodium symporter activity	IEA
GO:0015742	Process	Alpha-ketoglutarate transport	IEA
GO:0015746	Process	Citrate transport	IBA
GO:0015746	Process	Citrate transport	ISS
GO:0016020	Component	Membrane	IEA
GO:0016323	Component	Basolateral plasma membrane	IDA	27053689
GO:0017153	Function	Sodium:dicarboxylate symporter activity	IBA
GO:0017153	Function	Sodium:dicarboxylate symporter activity	IDA	10992006
GO:0017153	Function	Sodium:dicarboxylate symporter activity	TAS	10992006
GO:0022857	Function	Transmembrane transporter activity	IEA
GO:0034634	Function	Glutathione transmembrane transporter activity	IDA	24247155
GO:0034775	Process	Glutathione transmembrane transport	IDA	24247155
GO:0035725	Process	Sodium ion transmembrane transport	IEA
GO:0055085	Process	Transmembrane transport	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0071422	Process	Succinate transmembrane transport	IBA
GO:0071422	Process	Succinate transmembrane transport	IDA	10992006, 21264516, 24247155, 26176240
GO:0071422	Process	Succinate transmembrane transport	IEA
GO:0071422	Process	Succinate transmembrane transport	TAS	10992006
GO:0150104	Process	Transport across blood-brain barrier	NAS	30280653

MIM	HGNC	e!Ensembl
606411	14430	ENSG00000158296

Q8WWT9

Protein name

Na(+)/dicarboxylate cotransporter 3 (NaDC-3) (hNaDC3) (Na(+)-coupled carboxylate transporter 3) (NaC3) (Sodium-dependent high-affinity dicarboxylate transporter 2) (Solute carrier family 13 member 3) (SLC13A3)

Protein function

High-affinity sodium-dicarboxylate cotransporter that accepts a range of substrates with 4-6 carbon atoms, such as the citric acid cycle intermediates succinate and alpha-ketoglutarate (2-oxoglutarate), as well as other compounds including N-ace

PDB

8UVC , 8UVD , 8UVE , 8UVF , 8UVG , 8UVI

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00939	Na_sulph_symp	9 → 573	Sodium:sulfate symporter transmembrane region	Family

Tissue specificity

TISSUE SPECIFICITY: Expression is highest in kidney (PubMed:16331647). Detected in placenta, brain, liver and pancreas. {ECO:0000269|PubMed:16331647}.

Sequence

MAALAAAAKKVWSARRLLVLLFTPLALLPVVFALPPKEGRCLFVILLMAVYWCTEALPLS
VTALLPIVLFPFMGILPSNKVCPQYFLDTNFLFLSGLIMASAIEEWNLHRRIALKILMLV
GVQPARLILGMMVTTSFLSMWLSNTASTAMMLPIANAILKSLFGQKEVRKDPSQESEENT
AAVRRNGLHTVPTEMQFLASTEAKDHPGETEVPLDLPADSRKEDEYRRNIWKGFLISIPY
SASIGGTATLTGTAPNLILLGQLKSFFPQCDVVNFGSWFIFAFPLMLLFLLAGWLWISFL
YGGLSFRGWRKNKSEIRTNAEDRARAVIREEYQNLGPIKFAEQAVFILFCMFAILLFTRD
PKFIPGWASLFNPGFLSDAVTGVAIVTILFFFPSQRPSLKWWFDFKAPNTETEPLLTWKK
AQETVPWNIILLLGGGFAMAKGCEESGLSVWIGGQLHPLENVPPALAVLLITVVIAFFTE
FASNTATIIIFLPVLAELAIRLRVHPLYLMIPGTVGCSFAFMLPVSTPPNSIAFASGHLL
VKDMVRTGLLMNLMGVLLLSLAMNTWAQTIFQLGTFPDWADMYSVNVTALPPTLANDTFR
TL

Sequence length

602

Interactions

View interactions

	Reactome
			Sodium-coupled sulphate, di- and tri-carboxylate transporters

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Leukoencephalopathy, acute reversible, with increased urinary alpha-ketoglutarate	Likely pathogenic; Pathogenic	rs746862161, rs1568927501, rs1568904872	RCV003229502 RCV000767376 RCV000767377	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (7)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ASTROCYTOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC KIDNEY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prostate cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SLC13A3-related disorder	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (16)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Arthritis, Gouty	Gouty arthritis	GWASCAT_DG	22179738		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	26831905, 37657024	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral Infarction	Ischemic stroke	Pubtator	26352407	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Chronic Kidney Diseases	Kidney Disease	GWASDB_DG	24351856		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	18602983	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Gout	Gout	GWASCAT_DG	22179738		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hypertension Pulmonary	Pulmonary hypertension	Pubtator	26352407	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	37794328	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Failure Chronic	Kidney failure	Pubtator	18602983	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Failure, Chronic	Kidney Failure	GWASCAT_DG	24351856		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukoencephalopathy	Leukoencephalopathy	BEFREE	30635937		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus Systemic	Systemic lupus erythematosus	Pubtator	30777133	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	30037119		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteoarthritis Knee	Osteoarthritis	Pubtator	30086750	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	30037119		★★★★★ ★☆☆☆☆ Found in Text Mining only

SLC13A3 (solute carrier family 13 member 3)