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

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	6472
Gene name	Serine hydroxymethyltransferase 2
Gene symbol	SHMT2
Synonyms (NCBI Gene)	GLYAHEL-S-51eNEDCASBSHMTmSHMT
Chromosome	12
Chromosome location	12q13.3
Summary	This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is primarily responsible for glyci

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Show/Hide all (235)

miRTarBase ID	miRNA	Experiments	Reference
MIRT006985	hsa-miR-193b-3p	Luciferase reporter assay	21512034
MIRT006985	hsa-miR-193b-3p	Luciferase reporter assay	21512034
MIRT006985	hsa-miR-193b-3p	Reporter assay;Proteomics	21512034
MIRT006985	hsa-miR-193b-3p	Microarray	20304954
MIRT022109	hsa-miR-125b-5p	Other	20194440
MIRT022849	hsa-miR-124-3p	Proteomics;Microarray	18668037
MIRT052431	hsa-let-7a-5p	CLASH	23622248
MIRT049169	hsa-miR-92a-3p	CLASH	23622248
MIRT045122	hsa-miR-186-5p	CLASH	23622248
MIRT042617	hsa-miR-423-3p	CLASH	23622248
MIRT006985	hsa-miR-193b-3p	CLASH	23622248
MIRT040137	hsa-miR-615-3p	CLASH	23622248
MIRT036608	hsa-miR-940	CLASH	23622248
MIRT338626	hsa-miR-4428	PAR-CLIP	23592263
MIRT338629	hsa-miR-4716-3p	PAR-CLIP	23592263
MIRT338636	hsa-miR-6794-5p	PAR-CLIP	23592263
MIRT458226	hsa-miR-6805-5p	PAR-CLIP	23592263
MIRT458225	hsa-miR-6732-5p	PAR-CLIP	23592263
MIRT338631	hsa-miR-4726-3p	PAR-CLIP	23592263
MIRT458224	hsa-miR-7114-5p	PAR-CLIP	23592263
MIRT458223	hsa-miR-134-3p	PAR-CLIP	23592263
MIRT458222	hsa-miR-924	PAR-CLIP	23592263
MIRT338627	hsa-miR-4533	PAR-CLIP	23592263
MIRT338633	hsa-miR-5192	PAR-CLIP	23592263
MIRT458221	hsa-miR-3136-3p	PAR-CLIP	23592263
MIRT458220	hsa-miR-7155-3p	PAR-CLIP	23592263
MIRT338632	hsa-miR-4747-5p	PAR-CLIP	23592263
MIRT338634	hsa-miR-5196-5p	PAR-CLIP	23592263
MIRT458219	hsa-miR-2861	PAR-CLIP	23592263
MIRT338624	hsa-miR-4271	PAR-CLIP	23592263
MIRT338630	hsa-miR-4725-3p	PAR-CLIP	23592263
MIRT338637	hsa-miR-6780b-5p	PAR-CLIP	23592263
MIRT338620	hsa-miR-625-5p	PAR-CLIP	23592263
MIRT458218	hsa-miR-4417	PAR-CLIP	23592263
MIRT338625	hsa-miR-4278	PAR-CLIP	23592263
MIRT458217	hsa-miR-937-5p	PAR-CLIP	23592263
MIRT458216	hsa-miR-627-5p	PAR-CLIP	23592263
MIRT458214	hsa-miR-4265	PAR-CLIP	23592263
MIRT458215	hsa-miR-4296	PAR-CLIP	23592263
MIRT458213	hsa-miR-4322	PAR-CLIP	23592263
MIRT458212	hsa-miR-8081	PAR-CLIP	23592263
MIRT338626	hsa-miR-4428	PAR-CLIP	23592263
MIRT338629	hsa-miR-4716-3p	PAR-CLIP	23592263
MIRT338636	hsa-miR-6794-5p	PAR-CLIP	23592263
MIRT458226	hsa-miR-6805-5p	PAR-CLIP	23592263
MIRT458225	hsa-miR-6732-5p	PAR-CLIP	23592263
MIRT338631	hsa-miR-4726-3p	PAR-CLIP	23592263
MIRT458224	hsa-miR-7114-5p	PAR-CLIP	23592263
MIRT458223	hsa-miR-134-3p	PAR-CLIP	23592263
MIRT458222	hsa-miR-924	PAR-CLIP	23592263
MIRT338627	hsa-miR-4533	PAR-CLIP	23592263
MIRT338633	hsa-miR-5192	PAR-CLIP	23592263
MIRT458221	hsa-miR-3136-3p	PAR-CLIP	23592263
MIRT458220	hsa-miR-7155-3p	PAR-CLIP	23592263
MIRT338632	hsa-miR-4747-5p	PAR-CLIP	23592263
MIRT338634	hsa-miR-5196-5p	PAR-CLIP	23592263
MIRT458219	hsa-miR-2861	PAR-CLIP	23592263
MIRT338624	hsa-miR-4271	PAR-CLIP	23592263
MIRT338630	hsa-miR-4725-3p	PAR-CLIP	23592263
MIRT338637	hsa-miR-6780b-5p	PAR-CLIP	23592263
MIRT338620	hsa-miR-625-5p	PAR-CLIP	23592263
MIRT458218	hsa-miR-4417	PAR-CLIP	23592263
MIRT338625	hsa-miR-4278	PAR-CLIP	23592263
MIRT458217	hsa-miR-937-5p	PAR-CLIP	23592263
MIRT458216	hsa-miR-627-5p	PAR-CLIP	23592263
MIRT458214	hsa-miR-4265	PAR-CLIP	23592263
MIRT458215	hsa-miR-4296	PAR-CLIP	23592263
MIRT458213	hsa-miR-4322	PAR-CLIP	23592263
MIRT458212	hsa-miR-8081	PAR-CLIP	23592263
MIRT755599	hsa-miR-383-5p	Luciferase reporter assayWestern blottingqRT-PCRImmunohistochemistry (IHC)	38577602
MIRT1347438	hsa-miR-4300	CLIP-seq
MIRT1347439	hsa-miR-4321	CLIP-seq
MIRT1347440	hsa-miR-4536	CLIP-seq
MIRT1347441	hsa-miR-541	CLIP-seq
MIRT1347442	hsa-miR-654-5p	CLIP-seq
MIRT1347443	hsa-miR-920	CLIP-seq
MIRT1347444	hsa-miR-1470	CLIP-seq
MIRT1347445	hsa-miR-3126-5p	CLIP-seq
MIRT1347446	hsa-miR-3173-3p	CLIP-seq
MIRT1347447	hsa-miR-34b	CLIP-seq
MIRT1347448	hsa-miR-3688-3p	CLIP-seq
MIRT1347449	hsa-miR-4261	CLIP-seq
MIRT1347450	hsa-miR-4419a	CLIP-seq
MIRT1347451	hsa-miR-4476	CLIP-seq
MIRT1347452	hsa-miR-4510	CLIP-seq
MIRT1347453	hsa-miR-4643	CLIP-seq
MIRT1347454	hsa-miR-466	CLIP-seq
MIRT1347455	hsa-miR-4667-3p	CLIP-seq
MIRT1347456	hsa-miR-4779	CLIP-seq
MIRT1347457	hsa-miR-4789-3p	CLIP-seq
MIRT1347458	hsa-miR-510	CLIP-seq
MIRT1347459	hsa-miR-548ac	CLIP-seq
MIRT1347460	hsa-miR-548ae	CLIP-seq
MIRT1347461	hsa-miR-548aj	CLIP-seq
MIRT1347462	hsa-miR-548am	CLIP-seq
MIRT1347463	hsa-miR-548d-3p	CLIP-seq
MIRT1347464	hsa-miR-548x	CLIP-seq
MIRT1347465	hsa-miR-548z	CLIP-seq
MIRT1347466	hsa-miR-642a	CLIP-seq
MIRT2102869	hsa-miR-106a	CLIP-seq
MIRT2102870	hsa-miR-106b	CLIP-seq
MIRT2102871	hsa-miR-1237	CLIP-seq
MIRT2102872	hsa-miR-1248	CLIP-seq
MIRT2102873	hsa-miR-1254	CLIP-seq
MIRT2102874	hsa-miR-1264	CLIP-seq
MIRT2102875	hsa-miR-17	CLIP-seq
MIRT2102876	hsa-miR-20a	CLIP-seq
MIRT2102877	hsa-miR-20b	CLIP-seq
MIRT2102878	hsa-miR-296-5p	CLIP-seq
MIRT2102879	hsa-miR-3116	CLIP-seq
MIRT2102880	hsa-miR-3613-3p	CLIP-seq
MIRT2102881	hsa-miR-4263	CLIP-seq
MIRT2102882	hsa-miR-4290	CLIP-seq
MIRT1347455	hsa-miR-4667-3p	CLIP-seq
MIRT2102883	hsa-miR-515-3p	CLIP-seq
MIRT2102884	hsa-miR-519d	CLIP-seq
MIRT2102885	hsa-miR-519e	CLIP-seq
MIRT2102886	hsa-miR-550a	CLIP-seq
MIRT2102887	hsa-miR-625	CLIP-seq
MIRT2102888	hsa-miR-627	CLIP-seq
MIRT2102889	hsa-miR-661	CLIP-seq
MIRT2102890	hsa-miR-760	CLIP-seq
MIRT2102891	hsa-miR-93	CLIP-seq
MIRT2102869	hsa-miR-106a	CLIP-seq
MIRT2102870	hsa-miR-106b	CLIP-seq
MIRT2102871	hsa-miR-1237	CLIP-seq
MIRT2102872	hsa-miR-1248	CLIP-seq
MIRT2102873	hsa-miR-1254	CLIP-seq
MIRT2102874	hsa-miR-1264	CLIP-seq
MIRT2102875	hsa-miR-17	CLIP-seq
MIRT2102876	hsa-miR-20a	CLIP-seq
MIRT2102877	hsa-miR-20b	CLIP-seq
MIRT2102878	hsa-miR-296-5p	CLIP-seq
MIRT2102879	hsa-miR-3116	CLIP-seq
MIRT2327224	hsa-miR-3117-5p	CLIP-seq
MIRT2102881	hsa-miR-4263	CLIP-seq
MIRT2102882	hsa-miR-4290	CLIP-seq
MIRT1347455	hsa-miR-4667-3p	CLIP-seq
MIRT2327225	hsa-miR-4679	CLIP-seq
MIRT2102883	hsa-miR-515-3p	CLIP-seq
MIRT2102884	hsa-miR-519d	CLIP-seq
MIRT2102885	hsa-miR-519e	CLIP-seq
MIRT2102886	hsa-miR-550a	CLIP-seq
MIRT2102889	hsa-miR-661	CLIP-seq
MIRT2102891	hsa-miR-93	CLIP-seq
MIRT2327224	hsa-miR-3117-5p	CLIP-seq
MIRT2327225	hsa-miR-4679	CLIP-seq
MIRT2102869	hsa-miR-106a	CLIP-seq
MIRT2102870	hsa-miR-106b	CLIP-seq
MIRT2102871	hsa-miR-1237	CLIP-seq
MIRT2102872	hsa-miR-1248	CLIP-seq
MIRT2102873	hsa-miR-1254	CLIP-seq
MIRT2102874	hsa-miR-1264	CLIP-seq
MIRT2622483	hsa-miR-149	CLIP-seq
MIRT2102875	hsa-miR-17	CLIP-seq
MIRT2102876	hsa-miR-20a	CLIP-seq
MIRT2102877	hsa-miR-20b	CLIP-seq
MIRT2102878	hsa-miR-296-5p	CLIP-seq
MIRT2102879	hsa-miR-3116	CLIP-seq
MIRT2327224	hsa-miR-3117-5p	CLIP-seq
MIRT2622484	hsa-miR-3144-3p	CLIP-seq
MIRT2622485	hsa-miR-3148	CLIP-seq
MIRT2622486	hsa-miR-3156-5p	CLIP-seq
MIRT2622487	hsa-miR-3157-3p	CLIP-seq
MIRT2622488	hsa-miR-3192	CLIP-seq
MIRT2622489	hsa-miR-3202	CLIP-seq
MIRT2102880	hsa-miR-3613-3p	CLIP-seq
MIRT2102881	hsa-miR-4263	CLIP-seq
MIRT2622490	hsa-miR-4264	CLIP-seq
MIRT2102882	hsa-miR-4290	CLIP-seq
MIRT2622491	hsa-miR-4314	CLIP-seq
MIRT2622492	hsa-miR-4646-5p	CLIP-seq
MIRT1347455	hsa-miR-4667-3p	CLIP-seq
MIRT2327225	hsa-miR-4679	CLIP-seq
MIRT2622493	hsa-miR-4797-3p	CLIP-seq
MIRT2102883	hsa-miR-515-3p	CLIP-seq
MIRT2102884	hsa-miR-519d	CLIP-seq
MIRT2102885	hsa-miR-519e	CLIP-seq
MIRT2622494	hsa-miR-520d-5p	CLIP-seq
MIRT2622495	hsa-miR-524-5p	CLIP-seq
MIRT2102886	hsa-miR-550a	CLIP-seq
MIRT2622496	hsa-miR-619	CLIP-seq
MIRT2102887	hsa-miR-625	CLIP-seq
MIRT2102888	hsa-miR-627	CLIP-seq
MIRT2102889	hsa-miR-661	CLIP-seq
MIRT2102890	hsa-miR-760	CLIP-seq
MIRT2622497	hsa-miR-874	CLIP-seq
MIRT2622498	hsa-miR-875-5p	CLIP-seq
MIRT2102891	hsa-miR-93	CLIP-seq
MIRT2622499	hsa-miR-935	CLIP-seq
MIRT2622500	hsa-miR-942	CLIP-seq
MIRT2102869	hsa-miR-106a	CLIP-seq
MIRT2102870	hsa-miR-106b	CLIP-seq
MIRT2102871	hsa-miR-1237	CLIP-seq
MIRT2102872	hsa-miR-1248	CLIP-seq
MIRT2102873	hsa-miR-1254	CLIP-seq
MIRT2102874	hsa-miR-1264	CLIP-seq
MIRT2622483	hsa-miR-149	CLIP-seq
MIRT2102875	hsa-miR-17	CLIP-seq
MIRT2102876	hsa-miR-20a	CLIP-seq
MIRT2102877	hsa-miR-20b	CLIP-seq
MIRT2102878	hsa-miR-296-5p	CLIP-seq
MIRT2102879	hsa-miR-3116	CLIP-seq
MIRT2327224	hsa-miR-3117-5p	CLIP-seq
MIRT2622484	hsa-miR-3144-3p	CLIP-seq
MIRT2622485	hsa-miR-3148	CLIP-seq
MIRT2622486	hsa-miR-3156-5p	CLIP-seq
MIRT2622487	hsa-miR-3157-3p	CLIP-seq
MIRT2622488	hsa-miR-3192	CLIP-seq
MIRT2622489	hsa-miR-3202	CLIP-seq
MIRT2102880	hsa-miR-3613-3p	CLIP-seq
MIRT2102881	hsa-miR-4263	CLIP-seq
MIRT2622490	hsa-miR-4264	CLIP-seq
MIRT2102882	hsa-miR-4290	CLIP-seq
MIRT2622491	hsa-miR-4314	CLIP-seq
MIRT2622492	hsa-miR-4646-5p	CLIP-seq
MIRT1347455	hsa-miR-4667-3p	CLIP-seq
MIRT2327225	hsa-miR-4679	CLIP-seq
MIRT2622493	hsa-miR-4797-3p	CLIP-seq
MIRT2102883	hsa-miR-515-3p	CLIP-seq
MIRT2102884	hsa-miR-519d	CLIP-seq
MIRT2102885	hsa-miR-519e	CLIP-seq
MIRT2622494	hsa-miR-520d-5p	CLIP-seq
MIRT2622495	hsa-miR-524-5p	CLIP-seq
MIRT2102886	hsa-miR-550a	CLIP-seq
MIRT2622496	hsa-miR-619	CLIP-seq
MIRT2102887	hsa-miR-625	CLIP-seq
MIRT2102888	hsa-miR-627	CLIP-seq
MIRT2102889	hsa-miR-661	CLIP-seq
MIRT2102890	hsa-miR-760	CLIP-seq
MIRT2622497	hsa-miR-874	CLIP-seq
MIRT2622498	hsa-miR-875-5p	CLIP-seq
MIRT2102891	hsa-miR-93	CLIP-seq
MIRT2622499	hsa-miR-935	CLIP-seq
MIRT2622500	hsa-miR-942	CLIP-seq

Show/Hide all (68)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002082	Process	Regulation of oxidative phosphorylation	IEA
GO:0002082	Process	Regulation of oxidative phosphorylation	IMP	29364879, 29452640
GO:0003682	Function	Chromatin binding	IDA	18063578
GO:0004372	Function	Glycine hydroxymethyltransferase activity	IBA
GO:0004372	Function	Glycine hydroxymethyltransferase activity	IDA	8505317, 17482557, 24075985, 25619277, 29180469, 29364879, 29452640
GO:0004372	Function	Glycine hydroxymethyltransferase activity	IEA
GO:0004372	Function	Glycine hydroxymethyltransferase activity	IMP	33015733
GO:0005515	Function	Protein binding	IPI	19615732, 25416956, 25902260, 26871637, 29892012, 32296183, 33961781, 37398436
GO:0005634	Component	Nucleus	IDA	19513116, 24075985
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IDA	19513116, 24075985
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA	17482557, 19513116, 24075985
GO:0005739	Component	Mitochondrion	IEA
GO:0005743	Component	Mitochondrial inner membrane	IDA	21876188
GO:0005743	Component	Mitochondrial inner membrane	IEA
GO:0005743	Component	Mitochondrial inner membrane	TAS
GO:0005759	Component	Mitochondrial matrix	IDA	11516159, 21876188
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0006417	Process	Regulation of translation	IEA
GO:0006544	Process	Glycine metabolic process	IDA	25619277, 29180469
GO:0006544	Process	Glycine metabolic process	IEA
GO:0006544	Process	Glycine metabolic process	IGI	19513116
GO:0006544	Process	Glycine metabolic process	IMP	33015733
GO:0006545	Process	Glycine biosynthetic process	IEA
GO:0006563	Process	L-serine metabolic process	IDA	25619277, 29180469
GO:0006563	Process	L-serine metabolic process	IEA
GO:0006563	Process	L-serine metabolic process	IMP	33015733
GO:0006564	Process	L-serine biosynthetic process	IEA
GO:0006730	Process	One-carbon metabolic process	IDA	11516159, 29180469, 29364879, 29452640
GO:0006730	Process	One-carbon metabolic process	IEA
GO:0006730	Process	One-carbon metabolic process	IMP	33015733
GO:0008284	Process	Positive regulation of cell population proliferation	IEA
GO:0008732	Function	L-allo-threonine aldolase activity	IEA
GO:0015630	Component	Microtubule cytoskeleton	IDA
GO:0015943	Process	Formate biosynthetic process	IEA
GO:0016020	Component	Membrane	IEA
GO:0016597	Function	Amino acid binding	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0019264	Process	Glycine biosynthetic process from serine	IBA
GO:0019264	Process	Glycine biosynthetic process from serine	IEA
GO:0030170	Function	Pyridoxal phosphate binding	IBA
GO:0030170	Function	Pyridoxal phosphate binding	IDA	25619277
GO:0030170	Function	Pyridoxal phosphate binding	IEA
GO:0034340	Process	Response to type I interferon	IDA	24075985
GO:0035999	Process	Tetrahydrofolate interconversion	IEA
GO:0042645	Component	Mitochondrial nucleoid	IDA	18063578
GO:0042645	Component	Mitochondrial nucleoid	IEA
GO:0042802	Function	Identical protein binding	IEA
GO:0042802	Function	Identical protein binding	IPI	37398436
GO:0046653	Process	Tetrahydrofolate metabolic process	IBA
GO:0046653	Process	Tetrahydrofolate metabolic process	IDA	24075985, 25619277
GO:0046653	Process	Tetrahydrofolate metabolic process	IEA
GO:0051262	Process	Protein tetramerization	IDA	25619277
GO:0051289	Process	Protein homotetramerization	IDA	29180469
GO:0051289	Process	Protein homotetramerization	IEA
GO:0070013	Component	Intracellular organelle lumen	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867, 20458337
GO:0070129	Process	Regulation of mitochondrial translation	IEA
GO:0070129	Process	Regulation of mitochondrial translation	IMP	29364879, 29452640
GO:0070536	Process	Protein K63-linked deubiquitination	IMP	24075985
GO:0070552	Component	BRISC complex	IDA	24075985
GO:1903715	Process	Regulation of aerobic respiration	IEA
GO:1903715	Process	Regulation of aerobic respiration	IMP	29364879, 29452640

MIM	HGNC	e!Ensembl
138450	10852	ENSG00000182199

P34897

Protein name

Serine hydroxymethyltransferase, mitochondrial (SHMT) (EC 2.1.2.1) (Glycine hydroxymethyltransferase) (Serine methylase)

Protein function

Catalyzes the cleavage of serine to glycine accompanied with the production of 5,10-methylenetetrahydrofolate, an essential intermediate for purine biosynthesis (PubMed:24075985, PubMed:25619277, PubMed:29364879, PubMed:33015733). Serine provide

PDB

4PVF , 5V7I , 5X3V , 6DK3 , 6H3C , 6M5O , 6QVG , 6QVL , 6R8F , 7BYI , 8AQL , 8FJT , 8FJU , 8GKS , 8GKT , 8GKU , 8GKW , 8GKY , 8GKZ , 8QI7 , 8SSJ , 8T4O , 8T4P , 8TLC , 9BOX

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00464	SHMT	49 → 448	Serine hydroxymethyltransferase	Domain

Sequence

MLYFSLFWAARPLQRCGQLVRMAIRAQHSNAAQTQTGEANRGWTGQESLSDSDPEMWELL
QREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQ
RRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDV
KRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREV
CDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVD
PKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARA
MADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAIT
PGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQ
RLANLRQRVEQFARAFPMPGFDEH

Sequence length

504

Interactions

View interactions

	KEGG		Reactome
	Glycine, serine and threonine metabolism Glyoxylate and dicarboxylate metabolism One carbon pool by folate Metabolic pathways Carbon metabolism Biosynthesis of amino acids Biosynthesis of cofactors Antifolate resistance Folate transport and metabolism		Metabolism of folate and pterines

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 (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Neurodevelopmental disorder	Likely pathogenic	rs769908186, rs2037432429	RCV001374943 RCV001374944	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities	Likely pathogenic	rs2037465152, rs769908186, rs2037432429	RCV001270311 RCV001270316 RCV001270317	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (14)

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.
ANOREXIA NERVOSA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARCINOMA, NON-SMALL-CELL LUNG	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMPLEX NEURODEVELOPMENTAL DISORDER	—	GenCC	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBSESSIVE-COMPULSIVE DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SHMT2-related disorder	Conflicting classifications of pathogenicity; Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TOURETTE SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (64)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Acute Erythroblastic Leukemia	Erythroblastic Leukemia	BEFREE	31413099		★★★★★ ★☆☆☆☆ Found in Text Mining only
Anemia	Anemia	BEFREE	31690790		★★★★★ ★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	BEFREE	19440165		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	27666119, 29020998		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	27666119, 29020998, 31894856	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	34166228, 35018218, 35114976, 35798250, 37328520, 38188143	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	26662310, 31379360	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	20842733		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	35798250	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	36806313	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	37796681	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	Pubtator	40432803	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	30755591		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	23401104, 29886758, 30367038, 31773687		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	31773687, 35114976, 35211429, 40432803	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Degenerative polyarthritis	Arthritis	BEFREE	26103880		★★★★★ ★☆☆☆☆ Found in Text Mining only
Down Syndrome	Down Syndrome	BEFREE	21687976		★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal carcinoma	Esophageal Carcinoma	BEFREE	31773687		★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophagus Neoplasm	BEFREE	31773687		★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophageal neoplasm	Pubtator	31773687	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Gastrointestinal Neoplasms	Gastrointestinal Neoplasms	BEFREE	31773687		★★★★★ ★☆☆☆☆ Found in Text Mining only
Gastrointestinal Neoplasms	Gastrointestinal neoplasm	Pubtator	31773687	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	32203214, 36838582	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	28107674, 28794642		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	40432803	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Head and Neck Neoplasms	Head and neck neoplasm	Pubtator	36077112	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	32203214	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	37108312	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Idiopathic Pulmonary Fibrosis	Pulmonary Fibrosis	BEFREE	27836973		★★★★★ ★☆☆☆☆ Found in Text Mining only
Idiopathic Pulmonary Fibrosis	Idiopathic pulmonary fibrosis	Pubtator	27836973	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intrahepatic Cholangiocarcinoma	Intrahepatic Cholangiocarcinoma	BEFREE	30228815		★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney disease	Pubtator	37796681	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Neoplasms	Kidney neoplasm	Pubtator	33066813	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	25318605, 26662310, 27391339, 31379360		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	40508093	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	31581160	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	31773687, 35211429, 36077112, 40432803	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphoma	Lymphoma	Pubtator	33569544	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphoma, Non-Hodgkin	Non-Hodgkin lymphoma	BEFREE	21055808		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	27666119, 29020998		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of esophagus	Esophagus Neoplasm	BEFREE	31773687		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of liver	Liver Cancer	BEFREE	27391339, 31379360		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	20842733		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	31500219		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	31581160, 31773687		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	15044825, 24755469, 25132602, 27391339, 27666119, 28107674, 28794642, 29180469, 30228815, 30367038, 31773687		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	30755591		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	24700805, 25186948, 27391339, 27666119, 28107674, 28794642, 29180469, 30228815, 30367038, 31379360, 31773687		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	25186948		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	Pubtator	35018218	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	CTD_human_DG	26482881		★★★★★ ★☆☆☆☆ Found in Text Mining only
Ovarian Diseases	Ovarian diseases	Pubtator	37533289	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	25648260, 26438087		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	31500219		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	31500219	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Rhabdomyosarcoma	Rhabdomyosarcoma	Pubtator	34166228	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	31773687		★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	35333683	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of the head and neck	Carcinoma Of The Head And Neck	BEFREE	22051736		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	31581160, 31773687		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	31581160, 31773687, 38188143	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	37108312	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Thrombosis	Thrombosis	Pubtator	37328520	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Thyroid Cancer Papillary	Papillary thyroid cancer	Pubtator	38272883	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only

SHMT2 (serine hydroxymethyltransferase 2)