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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	284111
Gene name	Solute carrier family 13 member 5
Gene symbol	SLC13A5
Synonyms (NCBI Gene)	DEE25EIEE25INDYNACTmIndy
Chromosome	17
Chromosome location	17p13.1
Summary	This gene encodes a protein belonging to the solute carrier family 13 group of proteins. This family member is a sodium-dependent citrate cotransporter that may regulate metabolic processes. Mutations in this gene cause early infantile epileptic encephalo

Show/Hide all (27)

SNP ID	Visualize variation	Clinical significance	Consequence
rs144332569	C>T	Pathogenic-likely-pathogenic	Coding sequence variant, missense variant
rs150203483	C>T	Pathogenic	Stop gained, coding sequence variant
rs548065551	G>A	Pathogenic	Coding sequence variant, missense variant
rs587777577	G>A	Likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs587777578	A>G	Likely-pathogenic	Coding sequence variant, missense variant, intron variant, 3 prime UTR variant
rs730882222	A>C	Likely-pathogenic	Intron variant, splice donor variant
rs748950933	G>A,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs754553205	G>A,T	Conflicting-interpretations-of-pathogenicity, likely-benign, uncertain-significance	Coding sequence variant, synonymous variant, missense variant
rs761917087	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs773770609	G>A	Pathogenic	Stop gained, coding sequence variant
rs863225447	->ACTTTCTCCTG	Pathogenic	Coding sequence variant, frameshift variant
rs863225448	C>G	Pathogenic	Missense variant, intron variant, 3 prime UTR variant, coding sequence variant
rs966681982	T>C	Likely-pathogenic	Splice acceptor variant
rs1057517820	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs1057518298	C>T	Likely-pathogenic	Intron variant
rs1057518299	->G	Pathogenic	Frameshift variant, coding sequence variant
rs1057519449	A>G	Likely-pathogenic	3 prime UTR variant, coding sequence variant, intron variant, missense variant
rs1202091819	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1211773372	A>-	Likely-pathogenic	3 prime UTR variant, coding sequence variant, intron variant, frameshift variant
rs1555541483	C>T	Likely-pathogenic	Splice donor variant
rs1555541486	T>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1555543400	A>C,G	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant
rs1597653264	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant, intron variant, 3 prime UTR variant
rs1597657030	C>T	Likely-pathogenic	Splice acceptor variant
rs1597676610	A>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1597676674	C>T	Pathogenic	Coding sequence variant, stop gained
rs1597677742	C>T	Likely-pathogenic	Splice acceptor variant, intron variant

Show/Hide all (57)

miRTarBase ID	miRNA	Experiments
MIRT1352508	hsa-miR-1207-5p	CLIP-seq
MIRT1352509	hsa-miR-1306	CLIP-seq
MIRT1352510	hsa-miR-147	CLIP-seq
MIRT1352511	hsa-miR-1909	CLIP-seq
MIRT1352512	hsa-miR-2110	CLIP-seq
MIRT1352513	hsa-miR-3138	CLIP-seq
MIRT1352514	hsa-miR-3150a-3p	CLIP-seq
MIRT1352515	hsa-miR-3911	CLIP-seq
MIRT1352516	hsa-miR-4260	CLIP-seq
MIRT1352517	hsa-miR-4271	CLIP-seq
MIRT1352518	hsa-miR-4450	CLIP-seq
MIRT1352519	hsa-miR-4725-3p	CLIP-seq
MIRT1352520	hsa-miR-4736	CLIP-seq
MIRT1352521	hsa-miR-4763-3p	CLIP-seq
MIRT1352522	hsa-miR-4800-5p	CLIP-seq
MIRT1352523	hsa-miR-644	CLIP-seq
MIRT1352524	hsa-miR-937	CLIP-seq
MIRT1352508	hsa-miR-1207-5p	CLIP-seq
MIRT1352510	hsa-miR-147	CLIP-seq
MIRT1352511	hsa-miR-1909	CLIP-seq
MIRT1352512	hsa-miR-2110	CLIP-seq
MIRT1352513	hsa-miR-3138	CLIP-seq
MIRT1352514	hsa-miR-3150a-3p	CLIP-seq
MIRT1352525	hsa-miR-323-5p	CLIP-seq
MIRT1352526	hsa-miR-3650	CLIP-seq
MIRT1352515	hsa-miR-3911	CLIP-seq
MIRT1352516	hsa-miR-4260	CLIP-seq
MIRT1352517	hsa-miR-4271	CLIP-seq
MIRT1352518	hsa-miR-4450	CLIP-seq
MIRT1352527	hsa-miR-4505	CLIP-seq
MIRT1352519	hsa-miR-4725-3p	CLIP-seq
MIRT1352520	hsa-miR-4736	CLIP-seq
MIRT1352521	hsa-miR-4763-3p	CLIP-seq
MIRT1352522	hsa-miR-4800-5p	CLIP-seq
MIRT1352528	hsa-miR-629	CLIP-seq
MIRT1352523	hsa-miR-644	CLIP-seq
MIRT1352529	hsa-miR-876-3p	CLIP-seq
MIRT1352524	hsa-miR-937	CLIP-seq
MIRT1352525	hsa-miR-323-5p	CLIP-seq
MIRT2104366	hsa-miR-3652	CLIP-seq
MIRT2104367	hsa-miR-4430	CLIP-seq
MIRT1352527	hsa-miR-4505	CLIP-seq
MIRT2104368	hsa-miR-4793-5p	CLIP-seq
MIRT1352529	hsa-miR-876-3p	CLIP-seq
MIRT2328822	hsa-miR-122	CLIP-seq
MIRT2328823	hsa-miR-3198	CLIP-seq
MIRT2328824	hsa-miR-4309	CLIP-seq
MIRT2328825	hsa-miR-432	CLIP-seq
MIRT2328826	hsa-miR-574-5p	CLIP-seq
MIRT2328825	hsa-miR-432	CLIP-seq
MIRT2442630	hsa-miR-326	CLIP-seq
MIRT2442631	hsa-miR-330-5p	CLIP-seq
MIRT2442632	hsa-miR-3657	CLIP-seq
MIRT2442633	hsa-miR-4669	CLIP-seq
MIRT2623245	hsa-miR-103b	CLIP-seq
MIRT2623246	hsa-miR-4676-5p	CLIP-seq
MIRT2623247	hsa-miR-575	CLIP-seq

Show/Hide all (50)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005343	Function	Organic acid:sodium symporter activity	IDA	12445824, 26324167, 33597751
GO:0005343	Function	Organic acid:sodium symporter activity	IEA
GO:0005515	Function	Protein binding	IPI	28514442, 32296183, 33961781
GO:0005654	Component	Nucleoplasm	IDA
GO:0005829	Component	Cytosol	IDA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA	26384929
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	IMP	30054523
GO:0005886	Component	Plasma membrane	TAS
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006814	Process	Sodium ion transport	IEA
GO:0006842	Process	Tricarboxylic acid transport	IEA
GO:0015137	Function	Citrate transmembrane transporter activity	IBA
GO:0015137	Function	Citrate transmembrane transporter activity	IDA	21264516, 26176240
GO:0015137	Function	Citrate transmembrane transporter activity	IEA
GO:0015137	Function	Citrate transmembrane transporter activity	IMP	30054523
GO:0015137	Function	Citrate transmembrane transporter activity	TAS
GO:0015141	Function	Succinate transmembrane transporter activity	IBA
GO:0015141	Function	Succinate transmembrane transporter activity	IEA
GO:0015142	Function	Tricarboxylic acid transmembrane transporter activity	IEA
GO:0015293	Function	Symporter activity	IEA
GO:0015370	Function	Solute:sodium symporter activity	IEA
GO:0015729	Process	Oxaloacetate transport	IBA
GO:0015729	Process	Oxaloacetate transport	IDA	26324167
GO:0015729	Process	Oxaloacetate transport	IEA
GO:0015741	Process	Fumarate transport	IBA
GO:0015741	Process	Fumarate transport	IDA	26324167
GO:0015741	Process	Fumarate transport	IEA
GO:0015742	Process	Alpha-ketoglutarate transport	IDA	26324167
GO:0015742	Process	Alpha-ketoglutarate transport	IEA
GO:0015744	Process	Succinate transport	IBA
GO:0015744	Process	Succinate transport	IDA	26324167
GO:0015744	Process	Succinate transport	IEA
GO:0015746	Process	Citrate transport	IBA
GO:0015746	Process	Citrate transport	IDA	12445824, 21264516, 26176240, 26324167, 26384929, 33597751
GO:0015746	Process	Citrate transport	IEA
GO:0015746	Process	Citrate transport	IMP	30054523
GO:0016020	Component	Membrane	IEA
GO:0017153	Function	Sodium:dicarboxylate symporter activity	IBA
GO:0022857	Function	Transmembrane transporter activity	IEA
GO:0035674	Process	Tricarboxylic acid transmembrane transport	IEA
GO:0035725	Process	Sodium ion transmembrane transport	IEA
GO:0042802	Function	Identical protein binding	IPI	33597751
GO:0055085	Process	Transmembrane transport	IBA
GO:0055085	Process	Transmembrane transport	IEA
GO:0071285	Process	Cellular response to lithium ion	IDA	26324167
GO:0071285	Process	Cellular response to lithium ion	IEA
GO:0071422	Process	Succinate transmembrane transport	IEA
GO:1903825	Process	Organic acid transmembrane transport	IEA

MIM	HGNC	e!Ensembl
608305	23089	ENSG00000141485

Q86YT5

Protein name

Na(+)/citrate cotransporter (NaCT) (Sodium-coupled citrate transporter) (Sodium-dependent citrate transporter) (Solute carrier family 13 member 5)

Protein function

High-affinity sodium/citrate cotransporter that mediates the entry of citrate into cells, which is a critical participant of biochemical pathways (PubMed:12445824, PubMed:12826022, PubMed:26324167, PubMed:26384929, PubMed:30054523, PubMed:335977

PDB

7JSJ , 7JSK , 8UVB , 8UVH

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00939	Na_sulph_symp	8 → 554	Sodium:sulfate symporter transmembrane region	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed most predominantly in the liver, with moderate expression detectable in the brain and testis. {ECO:0000269|PubMed:12445824}.

Sequence

MASALSYVSKFKSFVILFVTPLLLLPLVILMPAKFVRCAYVIILMAIYWCTEVIPLAVTS
LMPVLLFPLFQILDSRQVCVQYMKDTNMLFLGGLIVAVAVERWNLHKRIALRTLLWVGAK
PARLMLGFMGVTALLSMWISNTATTAMMVPIVEAILQQMEATSAATEAGLELVDKGKAKE
LPGSQVIFEGPTLGQQEDQERKRLCKAMTLCICYAASIGGTATLTGTGPNVVLLGQMNEL
FPDSKDLVNFASWFAFAFPNMLVMLLFAWLWLQFVYMRFNFKKSWGCGLESKKNEKAALK
VLQEEYRKLGPLSFAEINVLICFFLLVILWFSRDPGFMPGWLTVAWVEGETKYVSDATVA
IFVATLLFIVPSQKPKFNFRSQTEEERKTPFYPPPLLDWKVTQEKVPWGIVLLLGGGFAL
AKGSEASGLSVWMGKQMEPLHAVPPAAITLILSLLVAVFTECTSNVATTTLFLPIFASMS
RSIGLNPLYIMLPCTLSASFAFMLPVATPPNAIVFTYGHLKVADMVKTGVIMNIIGVFCV
FLAVNTWGRAIFDLDHFPDWANVTHIET

Sequence length

568

Interactions

View interactions

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

644

Show/Hide Causal Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Chronic kidney disease	Likely pathogenic	rs730882222	RCV000162134
Developmental and epileptic encephalopathy, 25	Pathogenic; Likely pathogenic	rs2151485506, rs766330201, rs2150964787, rs113208940, rs144332569, rs587777577, rs587777578, rs2151495220, rs2544612394, rs2544638751, rs2544641047, rs2544624572, rs1973699766, rs2544660833, rs548065551 View all (23 more)	RCV001950878 RCV001913296 RCV001911536 RCV002047438 RCV000128860 RCV000128861 RCV000128862 RCV002221913 RCV002705962 RCV002893919 RCV002871768 RCV002890621 RCV002949386 RCV003026176 RCV000202396 RCV000202400 RCV000202392 RCV000202397 RCV000202401 RCV003026367 RCV000416469 RCV003586749 RCV003587880 RCV003749329 RCV003750064 RCV003847776 RCV003994688 RCV000416419 RCV001378440 RCV000526125 RCV001861705 RCV000807855 RCV000807588 RCV000989688 RCV000989691 RCV001040455 RCV001202622 RCV001201858
Epileptic encephalopathy	Likely pathogenic	rs1597653264, rs1597676610	RCV001003622 RCV001003623
Global developmental delay	Likely pathogenic	rs730882222	RCV000162134
Intellectual disability	Likely pathogenic; Pathogenic	rs761917087	RCV005625442
Seizure	Likely pathogenic	rs730882222	RCV000162134
SLC13A5-related disorder	Likely pathogenic; Pathogenic	rs548065551	RCV003955216
Undetermined early-onset epileptic encephalopathy	Likely pathogenic; Pathogenic	rs587777577	RCV000826127

Show/Hide Unknown Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cervical cancer	Likely benign	rs896810583	RCV005931437
Colon adenocarcinoma	Conflicting classifications of pathogenicity	rs754553205	RCV005898144
Familial cancer of breast	Likely benign	rs896810583	RCV005931435
Lung cancer	Likely benign	rs896810583	RCV005931439
Malignant tumor of esophagus	Likely benign	rs896810583	RCV005931436
Microcephaly	Uncertain significance	rs764711084	RCV001252851
Ovarian serous cystadenocarcinoma	Likely benign	rs896810583	RCV005931438
See cases	Conflicting classifications of pathogenicity	rs770640829	RCV002252301

Show/Hide Text Mining Associations (26)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Amelogenesis Imperfecta	Associate	33797191
Amelogenesis imperfecta local hypoplastic form	Associate	33797191
Brain Diseases	Associate	24995870, 30054523, 33797191, 39442909, 40577459
Carcinoma Hepatocellular	Associate	32634519
Carcinoma Renal Cell	Associate	22610075, 25332168
Developmental Disabilities	Associate	28673551, 33797191
Diarrhea 3 Secretory Sodium Congenital	Inhibit	33797191
Epilepsy	Associate	28673551, 32634519, 33597751, 33797191, 35633140
Epileptic Encephalopathy Early Infantile 3	Associate	35633140
Fever	Associate	33797191
Glioblastoma	Associate	21156036
Immunologic Deficiency Syndromes	Inhibit	33797191
Infantile Epileptic Dyskinetic Encephalopathy	Associate	28673551
Intellectual Disability	Associate	33797191
Kidney Diseases	Associate	38110950
Leukemia Lymphocytic Chronic B Cell	Associate	33336725
Melanoma Cutaneous Malignant	Associate	34755462
Metabolic Diseases	Associate	32634519
Metabolic Syndrome	Associate	34943889
Neurologic Manifestations	Associate	34943889
Obesity	Associate	33597751
Ovarian Neoplasms	Inhibit	36251340
Psychomotor Disorders	Associate	28673551
Renal Insufficiency Chronic	Associate	38110950
Seizures	Associate	24995870, 28673551, 35633140
Status Epilepticus	Associate	33797191

SLC13A5 (solute carrier family 13 member 5)