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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	54716
Gene name Gene Name - the full gene name approved by the HGNC.	Solute carrier family 6 member 20
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SLC6A20
Synonyms (NCBI Gene) Gene synonyms aliases	IMINO, SIT1, XT3, Xtrp3
Chromosome Chromosome number	3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	3p21.31
Summary Summary of gene provided in NCBI Entrez Gene.	Transport of small hydrophilic substances across cell membranes is mediated by substrate-specific transporter proteins which have been classified into several families of related genes. The protein encoded by this gene belongs to the sodium:neurotransmitt

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SNP ID	Visualize variation	Clinical significance	Consequence
rs17279437	G>A	Pathogenic, benign-likely-benign	Intron variant, missense variant, coding sequence variant

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miRTarBase ID	miRNA	Experiments	Reference
MIRT653449	hsa-miR-1228-3p	HITS-CLIP	23824327
MIRT653448	hsa-miR-6072	HITS-CLIP	23824327
MIRT653447	hsa-miR-6891-3p	HITS-CLIP	23824327
MIRT653446	hsa-miR-8064	HITS-CLIP	23824327
MIRT653445	hsa-miR-7702	HITS-CLIP	23824327
MIRT653444	hsa-miR-670-3p	HITS-CLIP	23824327
MIRT653443	hsa-miR-3074-5p	HITS-CLIP	23824327
MIRT653449	hsa-miR-1228-3p	HITS-CLIP	23824327
MIRT653448	hsa-miR-6072	HITS-CLIP	23824327
MIRT653447	hsa-miR-6891-3p	HITS-CLIP	23824327
MIRT653446	hsa-miR-8064	HITS-CLIP	23824327
MIRT653445	hsa-miR-7702	HITS-CLIP	23824327
MIRT653444	hsa-miR-670-3p	HITS-CLIP	23824327
MIRT653443	hsa-miR-3074-5p	HITS-CLIP	23824327
MIRT1366231	hsa-miR-1275	CLIP-seq
MIRT1366232	hsa-miR-3944-3p	CLIP-seq
MIRT1366233	hsa-miR-4492	CLIP-seq
MIRT1366234	hsa-miR-4498	CLIP-seq
MIRT1366235	hsa-miR-4505	CLIP-seq
MIRT1366236	hsa-miR-4525	CLIP-seq
MIRT1366237	hsa-miR-4665-5p	CLIP-seq
MIRT1366238	hsa-miR-4723-5p	CLIP-seq
MIRT1366239	hsa-miR-4731-5p	CLIP-seq
MIRT1366240	hsa-miR-625	CLIP-seq
MIRT1366241	hsa-miR-637	CLIP-seq
MIRT1366242	hsa-miR-762	CLIP-seq
MIRT1366243	hsa-miR-1224-3p	CLIP-seq
MIRT1366244	hsa-miR-1228	CLIP-seq
MIRT1366245	hsa-miR-124	CLIP-seq
MIRT1366246	hsa-miR-1245	CLIP-seq
MIRT1366247	hsa-miR-1279	CLIP-seq
MIRT1366248	hsa-miR-1293	CLIP-seq
MIRT1366249	hsa-miR-129-5p	CLIP-seq
MIRT1366250	hsa-miR-18a	CLIP-seq
MIRT1366251	hsa-miR-18b	CLIP-seq
MIRT1366252	hsa-miR-21	CLIP-seq
MIRT1366253	hsa-miR-2355-5p	CLIP-seq
MIRT1366254	hsa-miR-3138	CLIP-seq
MIRT1366255	hsa-miR-3170	CLIP-seq
MIRT1366256	hsa-miR-3194-3p	CLIP-seq
MIRT1366257	hsa-miR-3674	CLIP-seq
MIRT1366258	hsa-miR-3679-3p	CLIP-seq
MIRT1366259	hsa-miR-371-5p	CLIP-seq
MIRT1366260	hsa-miR-411	CLIP-seq
MIRT1366261	hsa-miR-4259	CLIP-seq
MIRT1366262	hsa-miR-4260	CLIP-seq
MIRT1366263	hsa-miR-4264	CLIP-seq
MIRT1366264	hsa-miR-4286	CLIP-seq
MIRT1366265	hsa-miR-431	CLIP-seq
MIRT1366266	hsa-miR-4328	CLIP-seq
MIRT1366267	hsa-miR-4443	CLIP-seq
MIRT1366268	hsa-miR-4446-5p	CLIP-seq
MIRT1366269	hsa-miR-4447	CLIP-seq
MIRT1366270	hsa-miR-4472	CLIP-seq
MIRT1366271	hsa-miR-4483	CLIP-seq
MIRT1366272	hsa-miR-450b-5p	CLIP-seq
MIRT1366273	hsa-miR-4653-3p	CLIP-seq
MIRT1366274	hsa-miR-4659a-3p	CLIP-seq
MIRT1366275	hsa-miR-4659b-3p	CLIP-seq
MIRT1366276	hsa-miR-4672	CLIP-seq
MIRT1366277	hsa-miR-4694-3p	CLIP-seq
MIRT1366278	hsa-miR-4698	CLIP-seq
MIRT1366279	hsa-miR-4703-3p	CLIP-seq
MIRT1366280	hsa-miR-4715-3p	CLIP-seq
MIRT1366281	hsa-miR-4715-5p	CLIP-seq
MIRT1366282	hsa-miR-4716-5p	CLIP-seq
MIRT1366283	hsa-miR-4732-5p	CLIP-seq
MIRT1366284	hsa-miR-4735-3p	CLIP-seq
MIRT1366285	hsa-miR-4735-5p	CLIP-seq
MIRT1366286	hsa-miR-4757-5p	CLIP-seq
MIRT1366287	hsa-miR-4761-5p	CLIP-seq
MIRT1366288	hsa-miR-4775	CLIP-seq
MIRT1366289	hsa-miR-4781-3p	CLIP-seq
MIRT1366290	hsa-miR-4793-5p	CLIP-seq
MIRT1366291	hsa-miR-4797-3p	CLIP-seq
MIRT1366292	hsa-miR-486-3p	CLIP-seq
MIRT1366293	hsa-miR-506	CLIP-seq
MIRT1366294	hsa-miR-590-3p	CLIP-seq
MIRT1366295	hsa-miR-590-5p	CLIP-seq
MIRT1366240	hsa-miR-625	CLIP-seq
MIRT1366296	hsa-miR-626	CLIP-seq
MIRT1366297	hsa-miR-627	CLIP-seq
MIRT1366298	hsa-miR-640	CLIP-seq
MIRT1366299	hsa-miR-759	CLIP-seq
MIRT1366300	hsa-miR-802	CLIP-seq
MIRT1366301	hsa-miR-924	CLIP-seq
MIRT1366289	hsa-miR-4781-3p	CLIP-seq
MIRT2108725	hsa-miR-3176	CLIP-seq
MIRT2108726	hsa-miR-3921	CLIP-seq
MIRT2108727	hsa-miR-3922-3p	CLIP-seq
MIRT2108728	hsa-miR-4653-5p	CLIP-seq
MIRT2108729	hsa-miR-4682	CLIP-seq
MIRT1366286	hsa-miR-4757-5p	CLIP-seq
MIRT1366291	hsa-miR-4797-3p	CLIP-seq
MIRT2108730	hsa-miR-642a	CLIP-seq
MIRT1366243	hsa-miR-1224-3p	CLIP-seq
MIRT1366246	hsa-miR-1245	CLIP-seq
MIRT1366231	hsa-miR-1275	CLIP-seq
MIRT2332356	hsa-miR-214	CLIP-seq
MIRT2332357	hsa-miR-3607-5p	CLIP-seq
MIRT2332358	hsa-miR-3613-3p	CLIP-seq
MIRT2332359	hsa-miR-3619-5p	CLIP-seq
MIRT2332360	hsa-miR-371b-5p	CLIP-seq
MIRT2332361	hsa-miR-3974	CLIP-seq
MIRT2332362	hsa-miR-3978	CLIP-seq
MIRT2332363	hsa-miR-4261	CLIP-seq
MIRT2332364	hsa-miR-4291	CLIP-seq
MIRT1366237	hsa-miR-4665-5p	CLIP-seq
MIRT2332365	hsa-miR-493	CLIP-seq
MIRT2332366	hsa-miR-494	CLIP-seq
MIRT1366298	hsa-miR-640	CLIP-seq
MIRT2332367	hsa-miR-761	CLIP-seq
MIRT2332368	hsa-miR-922	CLIP-seq
MIRT1366244	hsa-miR-1228	CLIP-seq
MIRT2442657	hsa-miR-3667-3p	CLIP-seq
MIRT2442658	hsa-miR-4778-3p	CLIP-seq
MIRT1366249	hsa-miR-129-5p	CLIP-seq
MIRT2459847	hsa-miR-296-5p	CLIP-seq
MIRT2459848	hsa-miR-3123	CLIP-seq
MIRT2459849	hsa-miR-3133	CLIP-seq
MIRT2459850	hsa-miR-3149	CLIP-seq
MIRT2459851	hsa-miR-3617	CLIP-seq
MIRT2459852	hsa-miR-3925-5p	CLIP-seq
MIRT2459853	hsa-miR-3973	CLIP-seq
MIRT2459854	hsa-miR-3976	CLIP-seq
MIRT1366260	hsa-miR-411	CLIP-seq
MIRT1366280	hsa-miR-4715-3p	CLIP-seq
MIRT1366285	hsa-miR-4735-5p	CLIP-seq
MIRT2459855	hsa-miR-4773	CLIP-seq
MIRT1366288	hsa-miR-4775	CLIP-seq
MIRT2459856	hsa-miR-539	CLIP-seq
MIRT2459857	hsa-miR-548l	CLIP-seq
MIRT1366294	hsa-miR-590-3p	CLIP-seq
MIRT2459858	hsa-miR-641	CLIP-seq
MIRT1366244	hsa-miR-1228	CLIP-seq
MIRT2626790	hsa-miR-204	CLIP-seq
MIRT2626791	hsa-miR-211	CLIP-seq
MIRT2626792	hsa-miR-302f	CLIP-seq
MIRT2459848	hsa-miR-3123	CLIP-seq
MIRT2626793	hsa-miR-3124-3p	CLIP-seq
MIRT1366256	hsa-miR-3194-3p	CLIP-seq
MIRT2459851	hsa-miR-3617	CLIP-seq
MIRT2442657	hsa-miR-3667-3p	CLIP-seq
MIRT1366258	hsa-miR-3679-3p	CLIP-seq
MIRT2459852	hsa-miR-3925-5p	CLIP-seq
MIRT2459853	hsa-miR-3973	CLIP-seq
MIRT2459854	hsa-miR-3976	CLIP-seq
MIRT2626794	hsa-miR-425	CLIP-seq
MIRT1366265	hsa-miR-431	CLIP-seq
MIRT1366268	hsa-miR-4446-5p	CLIP-seq
MIRT2626795	hsa-miR-4463	CLIP-seq
MIRT2626796	hsa-miR-4494	CLIP-seq
MIRT2626797	hsa-miR-4639-5p	CLIP-seq
MIRT2626798	hsa-miR-4755-5p	CLIP-seq
MIRT2442658	hsa-miR-4778-3p	CLIP-seq
MIRT2459856	hsa-miR-539	CLIP-seq
MIRT2459857	hsa-miR-548l	CLIP-seq
MIRT2626799	hsa-miR-623	CLIP-seq
MIRT2459858	hsa-miR-641	CLIP-seq
MIRT1366299	hsa-miR-759	CLIP-seq
MIRT1366300	hsa-miR-802	CLIP-seq
MIRT1366301	hsa-miR-924	CLIP-seq
MIRT1366244	hsa-miR-1228	CLIP-seq
MIRT1366249	hsa-miR-129-5p	CLIP-seq
MIRT2626790	hsa-miR-204	CLIP-seq
MIRT2626791	hsa-miR-211	CLIP-seq
MIRT2459848	hsa-miR-3123	CLIP-seq
MIRT2626793	hsa-miR-3124-3p	CLIP-seq
MIRT2459849	hsa-miR-3133	CLIP-seq
MIRT2459851	hsa-miR-3617	CLIP-seq
MIRT2442657	hsa-miR-3667-3p	CLIP-seq
MIRT2459852	hsa-miR-3925-5p	CLIP-seq
MIRT2459853	hsa-miR-3973	CLIP-seq
MIRT2459854	hsa-miR-3976	CLIP-seq
MIRT1366268	hsa-miR-4446-5p	CLIP-seq
MIRT1366280	hsa-miR-4715-3p	CLIP-seq
MIRT1366285	hsa-miR-4735-5p	CLIP-seq
MIRT2626798	hsa-miR-4755-5p	CLIP-seq
MIRT2459855	hsa-miR-4773	CLIP-seq
MIRT1366288	hsa-miR-4775	CLIP-seq
MIRT2442658	hsa-miR-4778-3p	CLIP-seq
MIRT2459856	hsa-miR-539	CLIP-seq
MIRT2459857	hsa-miR-548l	CLIP-seq
MIRT1366294	hsa-miR-590-3p	CLIP-seq
MIRT2626799	hsa-miR-623	CLIP-seq
MIRT2459858	hsa-miR-641	CLIP-seq
MIRT1366300	hsa-miR-802	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0005298	Function	Proline:sodium symporter activity	IBA
GO:0005298	Function	Proline:sodium symporter activity	IDA	33428810
GO:0005298	Function	Proline:sodium symporter activity	ISS	15632147
GO:0005515	Function	Protein binding	IPI	25416956, 32296183
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006865	Process	Amino acid transport	IDA	15632147
GO:0006865	Process	Amino acid transport	IEA
GO:0006865	Process	Amino acid transport	TAS
GO:0015171	Function	Amino acid transmembrane transporter activity	IDA	15632147
GO:0015171	Function	Amino acid transmembrane transporter activity	ISS	15632147
GO:0015171	Function	Amino acid transmembrane transporter activity	TAS
GO:0015175	Function	Neutral L-amino acid transmembrane transporter activity	IMP	19033659
GO:0015175	Function	Neutral L-amino acid transmembrane transporter activity	ISS
GO:0015188	Function	L-isoleucine transmembrane transporter activity	ISS	16234310
GO:0015193	Function	L-proline transmembrane transporter activity	IBA
GO:0015193	Function	L-proline transmembrane transporter activity	IDA	15632147
GO:0015193	Function	L-proline transmembrane transporter activity	IGI	25534429
GO:0015199	Function	Amino-acid betaine transmembrane transporter activity	ISS
GO:0015293	Function	Symporter activity	IEA
GO:0015370	Function	Solute:sodium symporter activity	IDA	33428810
GO:0015816	Process	Glycine transport	IMP	19033659
GO:0015824	Process	Proline transport	IMP	19033659
GO:0015838	Process	Amino-acid betaine transport	ISS
GO:0016020	Component	Membrane	IEA
GO:0016324	Component	Apical plasma membrane	IBA
GO:0016324	Component	Apical plasma membrane	IDA	25534429
GO:0016324	Component	Apical plasma membrane	IEA
GO:0016324	Component	Apical plasma membrane	ISS
GO:0022857	Function	Transmembrane transporter activity	IEA
GO:0035725	Process	Sodium ion transmembrane transport	IBA
GO:0089718	Process	Amino acid import across plasma membrane	ISS	15632147
GO:0150104	Process	Transport across blood-brain barrier	NAS	30280653
GO:1903804	Process	Glycine import across plasma membrane	IBA
GO:1903804	Process	Glycine import across plasma membrane	IDA	33428810
GO:1903806	Process	L-isoleucine import across plasma membrane	ISS	16234310
GO:1904271	Process	L-proline import across plasma membrane	IBA
GO:1904271	Process	L-proline import across plasma membrane	IDA	15632147, 33428810
GO:1904271	Process	L-proline import across plasma membrane	IGI	25534429
GO:1905647	Process	Proline import across plasma membrane	IMP	19033659

MIM	HGNC	e!Ensembl
605616	30927	ENSG00000163817

Protein

UniProt ID

Q9NP91

Protein name

Sodium- and chloride-dependent transporter XTRP3 (Sodium/imino-acid transporter 1) (Solute carrier family 6 member 20) (Transporter rB21A homolog)

Protein function

Mediates the Na(+)- and Cl(-)-dependent uptake of imino acids such as L-proline, N-methyl-L-proline and pipecolate as well as N-methylated amino acids (PubMed:15632147, PubMed:19033659, PubMed:33428810). Also transports glycine, regulates prolin

PDB

7Y75 , 7Y76 , 8I91 , 8P2W , 8P2X , 8P2Y , 8P2Z , 8P30 , 8P31 , 8WM3

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00209	SNF	5 → 581	Sodium:neurotransmitter symporter family	Family

Tissue specificity

TISSUE SPECIFICITY: Kidney and small intestine. Expressed in the S3 segment of the proximal tubule. Expressed in neurons (PubMed:33428810). {ECO:0000269|PubMed:19033659, ECO:0000269|PubMed:33428810, ECO:0000269|PubMed:9932288}.

Sequence

MEKARPLWANSLQFVFACISYAVGLGNVWRFPYLCQMYGGGSFLVPYIIMLIVEGMPLLY
LELAVGQRMRQGSIGAWRTISPYLSGVGVASVVVSFFLSMYYNVINAWAFWYLFHSFQDP
LPWSVCPLNGNHTGYDEECEKASSTQYFWYRKTLNISPSLQENGGVQWEPALCLLLAWLV
VYLCILRGTESTGKVVYFTASLPYCVLIIYLIRGLTLHGATNGLMYMFTPKIEQLANPKA
WINAATQIFFSLGLGFGSLIAFASYNEPSNNCQKHAIIVSLINSFTSIFASIVTFSIYGF
KATFNYENCLKKVSLLLTNTFDLEDGFLTASNLEQVKGYLASAYPSKYSEMFPQIKNCSL
ESELDTAVQGTGLAFIVYTEAIKNMEVSQLWSVLYFFMLLMLGIGSMLGNTAAILTPLTD
SKIISSHLPKEAISGLVCLVNCAIGMVFTMEAGNYWFDIFNDYAATLSLLLIVLVETIAV
CYVYGLRRFESDLKAMTGRAVSWYWKVMWAGVSPLLIVSLFVFYLSDYILTGTLKYQAWD
ASQGQLVTKDYPAYALAVIGLLVASSTMCIPLAALGTFVQRRLKRGDADPVA

Sequence length

592

Interactions

View interactions

	Reactome
			Amino acid transport across the plasma membrane Na+/Cl- dependent neurotransmitter transporters Variant SLC6A20 contributes towards hyperglycinuria (HG) and iminoglycinuria (IG) Variant SLC6A20 contributes towards hyperglycinuria (HG) and iminoglycinuria (IG)

Show/Hide Unknown Diseases (3)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Hirschsprung Disease	Hirschsprung disease	N/A	N/A	GWAS
hyperglycinuria	Hyperglycinuria	N/A	N/A	ClinVar
Oligodendroglioma	Oligodendroglioma	N/A	N/A	GWAS

Show/Hide Text Mining Associations (17)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
2 Methylbutyryl CoA Dehydrogenase Deficiency	Associate	35236679
Alzheimer Disease	Associate	30535121
COVID 19	Associate	32899439, 33164753, 33604698, 34425859, 34969185, 35212764, 35261286, 36292769, 37085563, 37160831, 39344392
Diabetes Mellitus Type 2	Associate	30535121, 34969185
Hereditary Breast and Ovarian Cancer Syndrome	Associate	30535121
Hirschsprung Disease	Associate	25310821, 31358688
Iminoglycinuria	Associate	19033659
Mesothelioma Malignant	Associate	17659810
Myopia	Associate	30535121
Neoplasms	Associate	30535121
Neurodegenerative Diseases	Associate	30535121
Obesity	Associate	39344392
Parkinson Disease	Associate	30535121
Polyps	Associate	37085563
Schizophrenia	Associate	30535121
Urinary Bladder Neoplasms	Associate	22529986
Virus Diseases	Associate	35261286

SLC6A20 (solute carrier family 6 member 20)