GLDC (glycine decarboxylase)

Gene

• Entrez ID: 2731
• Gene name: Glycine decarboxylase
• Gene symbol: GLDC
• Synonyms (NCBI Gene): GCE, GCE1, GCSP, HYGN1
• Chromosome: 9
• Chromosome location: 9p24.1
• Summary: Degradation of glycine is brought about by the glycine cleavage system, which is composed of four mitochondrial protein components: P protein (a pyridoxal phosphate-dependent glycine decarboxylase), H protein (a lipoic acid-containing protein), T protein

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121964974	C>A	Pathogenic	Coding sequence variant, missense variant
rs121964975	AAG>-	Pathogenic-likely-pathogenic	Coding sequence variant, inframe deletion
rs121964976	C>G,T	Pathogenic, benign	Coding sequence variant, synonymous variant, missense variant
rs121964977	G>A	Pathogenic	Coding sequence variant, missense variant
rs121964978	A>G	Pathogenic	Initiator codon variant, missense variant
rs121964979	G>A,T	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs121964980	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs140877566	G>A,C	Conflicting-interpretations-of-pathogenicity, likely-benign	Intron variant
rs144090917	C>G,T	Conflicting-interpretations-of-pathogenicity, benign	Missense variant, coding sequence variant
rs149070244	C>G,T	Pathogenic-likely-pathogenic, pathogenic	Splice donor variant
rs150171524	G>A,C	Conflicting-interpretations-of-pathogenicity, pathogenic	Missense variant, coding sequence variant
rs151163582	C>A	Likely-pathogenic	Missense variant, coding sequence variant
rs151268759	C>A,G,T	Likely-pathogenic, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs188269735	A>C	Pathogenic	Missense variant, coding sequence variant
rs191905539	C>A	Pathogenic	Coding sequence variant, stop gained
rs201135624	G>A	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs367781728	G>A,C	Likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs373618804	T>A	Likely-pathogenic	Stop gained, coding sequence variant
rs386833516	->A	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833517	G>A,C	Pathogenic	Stop gained, missense variant, coding sequence variant
rs386833518	T>-	Pathogenic-likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant
rs386833519	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833520	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833521	G>A	Pathogenic-likely-pathogenic	Stop gained, coding sequence variant
rs386833522	->TTTG	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833523	A>G,T	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs386833524	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs386833525	C>G	Likely-pathogenic	Splice acceptor variant
rs386833526	->C	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833527	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833528	T>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833529	T>C	Pathogenic	Missense variant, coding sequence variant
rs386833530	C>G,T	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs386833531	G>A	Pathogenic-likely-pathogenic	Stop gained, coding sequence variant
rs386833532	GTCATAACCTG>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833533	A>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833534	C>T	Likely-pathogenic	Splice donor variant
rs386833535	C>A,T	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs386833536	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833537	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs386833538	C>G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833539	G>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833540	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833541	GAT>TAAACCAGGA	Likely-pathogenic	Stop gained, inframe indel, coding sequence variant
rs386833542	C>G,T	Likely-pathogenic	Missense variant, coding sequence variant
rs386833543	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs386833544	A>T	Likely-pathogenic	Missense variant, coding sequence variant
rs386833545	T>C	Pathogenic	Splice acceptor variant
rs386833546	CA>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833547	T>G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833549	C>G,T	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs386833550	C>T	Pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs386833551	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833552	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833553	C>T	Pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs386833554	C>T	Pathogenic	Splice acceptor variant
rs386833555	T>A,C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833556	G>A,C	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs386833557	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs386833558	T>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833559	A>C,G	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs386833560	G>A	Pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs386833563	C>T	Likely-pathogenic	Splice donor variant
rs386833564	A>C,G	Likely-pathogenic	Stop gained, synonymous variant, coding sequence variant
rs386833565	G>T	Pathogenic	Synonymous variant, coding sequence variant
rs386833566	T>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833567	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs386833568	C>T	Likely-pathogenic	Intron variant
rs386833569	C>G	Likely-pathogenic	Splice acceptor variant
rs386833570	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833571	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833572	->T	Likely-pathogenic	Stop gained, coding sequence variant
rs386833573	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833574	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833575	C>G,T	Pathogenic	Splice donor variant
rs386833576	G>A,C,T	Likely-pathogenic	Stop gained, missense variant, coding sequence variant
rs386833577	T>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833578	T>C,G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833579	C>A	Likely-pathogenic	Stop gained, coding sequence variant
rs386833580	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833581	C>G	Likely-pathogenic	Synonymous variant, coding sequence variant
rs386833582	G>A,C,T	Likely-pathogenic	Missense variant, coding sequence variant
rs386833583	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs386833584	C>A,T	Likely-pathogenic	Missense variant, coding sequence variant
rs386833585	G>A,C	Likely-pathogenic	Stop gained, missense variant, coding sequence variant
rs386833586	G>-	Pathogenic-likely-pathogenic	Frameshift variant, coding sequence variant
rs386833587	G>A	Pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs386833588	C>A	Likely-pathogenic	Stop gained, coding sequence variant
rs386833589	C>G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833590	C>A	Likely-pathogenic	Splice donor variant
rs386833591	A>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833592	C>A,G,T	Likely-pathogenic	Missense variant, coding sequence variant
rs386833593	G>T	Likely-pathogenic	Missense variant, coding sequence variant
rs542056100	C>T	Pathogenic	Splice donor variant
rs570097430	G>A,T	Likely-pathogenic	Stop gained, missense variant, coding sequence variant
rs751025203	G>A	Pathogenic	Coding sequence variant, stop gained
rs751822565	C>A	Pathogenic-likely-pathogenic	Coding sequence variant, missense variant
rs755313904	->GAAC	Pathogenic, likely-pathogenic	Coding sequence variant, frameshift variant
rs759133707	C>T	Pathogenic	Coding sequence variant, missense variant
rs762989914	G>A	Pathogenic	Coding sequence variant, stop gained
rs763517274	C>G,T	Likely-pathogenic	Coding sequence variant, missense variant
rs765906340	C>G,T	Pathogenic	Splice donor variant
rs766762760	GTTT>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs768091555	C>A	Likely-pathogenic	Intron variant
rs769625871	TGC>-	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, inframe deletion
rs772068893	->AT	Pathogenic-likely-pathogenic	Coding sequence variant, frameshift variant
rs772574530	T>C	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant
rs772871471	G>C	Likely-pathogenic	Coding sequence variant, missense variant
rs774099283	C>A,G	Likely-pathogenic	Splice donor variant
rs777365335	C>A,G	Likely-pathogenic	Coding sequence variant, missense variant, stop gained
rs906049409	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs925908885	C>T	Pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs978795483	C>A,G	Likely-pathogenic, pathogenic	Splice donor variant
rs1114167353	A>T	Pathogenic	Coding sequence variant, missense variant
rs1163356968	C>G,T	Pathogenic	Coding sequence variant, missense variant, stop gained
rs1183976692	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1196401015	ATGATAGC>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1207147043	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1211616091	C>T	Likely-pathogenic	Splice donor variant
rs1226098656	G>A,T	Likely-pathogenic	Synonymous variant, stop gained, coding sequence variant
rs1251443902	T>-	Pathogenic-likely-pathogenic	Coding sequence variant, frameshift variant
rs1259354298	T>C	Likely-pathogenic	Splice acceptor variant
rs1345599468	A>-	Pathogenic	Frameshift variant, coding sequence variant
rs1368757896	C>G,T	Likely-pathogenic	Splice donor variant
rs1399754800	C>-	Likely-pathogenic	Splice donor variant, coding sequence variant
rs1406713104	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1429861000	C>T	Likely-pathogenic	Splice acceptor variant
rs1430968530	T>A	Pathogenic-likely-pathogenic	Stop gained, coding sequence variant
rs1477860542	C>A,T	Likely-pathogenic	Missense variant, coding sequence variant, stop gained
rs1554641737	->G	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1554641887	A>G	Pathogenic-likely-pathogenic	Splice donor variant
rs1554642300	->G	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1554643354	G>C	Pathogenic	Coding sequence variant, stop gained
rs1554643360	G>A	Pathogenic	Coding sequence variant, stop gained
rs1554643370	C>A	Likely-pathogenic	Splice acceptor variant
rs1554643619	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1554643738	A>T	Likely-pathogenic	Splice donor variant
rs1554644678	C>T	Likely-pathogenic	Intron variant
rs1554646529	C>A	Pathogenic, likely-pathogenic	Coding sequence variant, stop gained
rs1554646653	G>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1554646710	A>C	Pathogenic	Splice donor variant
rs1554648060	G>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1554649675	C>G	Likely-pathogenic	Splice acceptor variant
rs1554652870	G>A,T	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant, stop gained
rs1563834980	->G	Pathogenic	Coding sequence variant, frameshift variant
rs1563849699	CTG>-	Likely-pathogenic	Coding sequence variant, inframe deletion
rs1563864784	->TATT	Pathogenic	Coding sequence variant, frameshift variant
rs1587922096	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1587950355	C>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1587951033	A>-	Pathogenic	Frameshift variant, coding sequence variant
rs1587958061	C>A	Pathogenic	Splice acceptor variant
rs1587959976	A>T	Pathogenic	Splice donor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT042509	hsa-miR-423-3p	CLASH	23622248
MIRT042509	hsa-miR-423-3p	CLASH	23622248
MIRT2235284	hsa-miR-3190	CLIP-seq
MIRT2235285	hsa-miR-4491	CLIP-seq
MIRT2235286	hsa-miR-4657	CLIP-seq
MIRT2235287	hsa-miR-671-5p	CLIP-seq
MIRT2539021	hsa-miR-1304	CLIP-seq
MIRT2539022	hsa-miR-143	CLIP-seq
MIRT2539023	hsa-miR-2467-5p	CLIP-seq
MIRT2539024	hsa-miR-3188	CLIP-seq
MIRT2539025	hsa-miR-342-5p	CLIP-seq
MIRT2539026	hsa-miR-3975	CLIP-seq
MIRT2539027	hsa-miR-4505	CLIP-seq
MIRT2539028	hsa-miR-4651	CLIP-seq
MIRT2539029	hsa-miR-4664-5p	CLIP-seq
MIRT2539030	hsa-miR-4731-5p	CLIP-seq
MIRT2539031	hsa-miR-4770	CLIP-seq
MIRT2539032	hsa-miR-485-5p	CLIP-seq
MIRT2539033	hsa-miR-608	CLIP-seq
MIRT2539021	hsa-miR-1304	CLIP-seq
MIRT2539022	hsa-miR-143	CLIP-seq
MIRT2539023	hsa-miR-2467-5p	CLIP-seq
MIRT2539024	hsa-miR-3188	CLIP-seq
MIRT2539025	hsa-miR-342-5p	CLIP-seq
MIRT2539026	hsa-miR-3975	CLIP-seq
MIRT2539027	hsa-miR-4505	CLIP-seq
MIRT2539028	hsa-miR-4651	CLIP-seq
MIRT2539029	hsa-miR-4664-5p	CLIP-seq
MIRT2539030	hsa-miR-4731-5p	CLIP-seq
MIRT2539031	hsa-miR-4770	CLIP-seq
MIRT2539032	hsa-miR-485-5p	CLIP-seq
MIRT2539033	hsa-miR-608	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004375	Function	Glycine dehydrogenase (decarboxylating) activity	IBA
GO:0004375	Function	Glycine dehydrogenase (decarboxylating) activity	IDA	28244183
GO:0004375	Function	Glycine dehydrogenase (decarboxylating) activity	IEA
GO:0004375	Function	Glycine dehydrogenase (decarboxylating) activity	TAS	1996985
GO:0005654	Component	Nucleoplasm	IDA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA	28244183
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0005886	Component	Plasma membrane	IDA
GO:0005960	Component	Glycine cleavage complex	IBA
GO:0006520	Process	Amino acid metabolic process	IEA
GO:0006544	Process	Glycine metabolic process	IEA
GO:0006546	Process	Glycine catabolic process	IDA	28244183
GO:0006546	Process	Glycine catabolic process	IEA
GO:0006546	Process	Glycine catabolic process	TAS	1996985
GO:0009055	Function	Electron transfer activity	TAS	2268343
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0016594	Function	Glycine binding	IBA
GO:0016829	Function	Lyase activity	IEA
GO:0019464	Process	Glycine decarboxylation via glycine cleavage system	IBA
GO:0030170	Function	Pyridoxal phosphate binding	IBA
GO:0036255	Process	Response to methylamine	ISS
GO:0042803	Function	Protein homodimerization activity	ISS
GO:0070280	Function	Pyridoxal binding	ISS
GO:1903442	Process	Response to lipoic acid	ISS
GO:1990830	Process	Cellular response to leukemia inhibitory factor	IEA

Other IDs

• MIM: 238300
• HGNC: 4313
• e!Ensembl: ENSG00000178445

Protein

• UniProt ID: P23378
• Protein name: Glycine dehydrogenase (decarboxylating), mitochondrial (EC 1.4.4.2) (Glycine cleavage system P protein) (Glycine decarboxylase) (Glycine dehydrogenase (aminomethyl-transferring))
• Protein function: The glycine cleavage system catalyzes the degradation of glycine. The P protein (GLDC) binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to
• PDB: 6I33, 6I34, 6I35
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02347	GDC-P	65 → 488	Glycine cleavage system P-protein	Domain
  PF01212	Beta_elim_lyase	584 → 743	Beta-eliminating lyase	Domain

• Sequence:

  MQSCARAWGLRLGRGVGGGRRLAGGSGPCWAPRSRDSSSGGGDSAAAGASRLLERLLPRH
  DDFARRHIGPGDKDQREMLQTLGLASIDELIEKTVPANIRLKRPLKMEDPVCENEILATL
  HAISSKNQIWRSYIGMGYYNCSVPQTILRNLLENSGWITQYTPYQPEVSQGRLESLLNYQ
  TMVCDITGLDMANASLLDEGTAAAEALQLCYRHNKRRKFLVDPRCHPQTIAVVQTRAKYT
  GVLTELKLPCEMDFSGKDVSGVLFQYPDTEGKVEDFTELVERAHQSGSLACCATDLLALC
  ILRPPGEFGVDIALGSSQRFGVPLGYGGPHAAFFAVRESLVRMMPGRMVGVTRDATGKEV
  YRLALQTREQHIRRDKATSNICTAQALLANMAAMFAIYHGSHGLEHIARRVHNATLILSE
  GLKRAGHQLQHDLFFDTLKIQCGCSVKEVLGRAAQRQINFRLFEDGTLGISLDETVNEKD
  LDDLLWIFGCESSAELVAESMGEECRGIPGSVFKRTSPFLTHQVFNSYHSETNIVRYMKK
  LENKDISLVHSMIPLGSCTMKLNSSSELAPITWKEFANIHPFVPLDQAQGYQQLFRELEK
  DLCELTGYDQVCFQPNSGAQGEYAGLATIRAYLNQKGEGHRTVCLIPKSAHGTNPASAHM
  AGMKIQPVEVDKYGNIDAVHLKAMVDKHKENLAAIMITYPSTNGVFEENISDVCDLIHQH
  GGQVYLDGANMNAQVGICRPGDFGSDVSHLNLHKTFCIPHGGGGPGMGPIGVKKHLAPFL
  PNHPVISLKRNEDACPVGTVSAAPWGSSSILPISWAYIKMMGGKGLKQATETAILNANYM
  AKRLETHYRILFRGARGYVGHEFILDTRPFKKSANIEAVDVAKRLQDYGFHAPTMSWPVA
  GTLMVEPTESEDKAELDRFCDAMISIRQEIADIEEGRIDPRVNPLKMSPHSLTCVTSSHW
  DRPYSREVAAFPLPFVKPENKFWPTIARIDDIYGDQHLVCTCPPMEVYESPFSEQKRASS
  

• Sequence length: 1020

Pathways

KEGG:

Glycine, serine and threonine metabolism
Glyoxylate and dicarboxylate metabolism
One carbon pool by folate
Lipoic acid metabolism
Metabolic pathways
Carbon metabolism

Reactome:

Glycine degradation

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Generalized epilepsy	Pathogenic	rs121964976	RCV000449527
GLDC-related disorder	Pathogenic; Likely pathogenic	rs121964976, rs191905539, rs1163356968, rs386833518, rs386833521, rs386833524, rs386833554, rs386833557, rs386833580	RCV003398490 RCV004745365 RCV003983163 RCV003415813 RCV004745180 RCV003407429 RCV003415814 RCV003390751 RCV003974936
Global developmental delay	Pathogenic	rs121964976	RCV000449527
Glycine encephalopathy	Likely pathogenic; Pathogenic	rs1818705322, rs2129898042, rs1818463608, rs758575745, rs367987650, rs2129719653, rs1818287644, rs2129663304, rs1447727878, rs2129725961, rs2129831711, rs959935793, rs2129896575, rs777632051, rs2129897960, rs2129916235, rs2129916327, rs2130031690, rs2130032358, rs121964978, rs147951756, rs1554643738, rs386833583, rs1819058509, rs1817625926, rs2129831443, rs1452327155, rs1817122724, rs2129758198, rs1170385434, rs2130032664, rs2130029354, rs1300550278, rs2129719586, rs2129735272, rs1417674040, rs386833578, rs2129948795, rs1288008254, rs2129898271, rs2129649998, rs2130029228, rs2129649871, rs1272244088, rs2129758221, rs2130029302, rs2129831448, rs1374110692, rs2129949245, rs2129714616, rs2129837171, rs2129898670, rs148775220, rs1818317328, rs2129645358, rs2129885269, rs2129649366, rs774506115, rs2129850481, rs1227030484, rs570097430, rs1563859767, rs1172061571, rs1209943477, rs2129948971, rs2129916293, rs2129650066, rs2129885505, rs2129726392, rs1264725941, rs1587946346, rs747853668, rs1817583687, rs1207147043, rs2129645235, rs2129916678, rs149070244, rs2129895643, rs2129735367, rs2129725849, rs1323060528, rs386833525, rs763075374, rs1368757896, rs2489079135, rs2489036171, rs1383111309, rs2489111102, rs2489080277, rs2489085288, rs2489011454, rs2489031850, rs2489104302, rs2489124599, rs2489048081, rs2489011561, rs2489110995, rs2489076733, rs1458411946, rs2489076677, rs2489104369, rs2489036370, rs2489085220, rs2489160614, rs2489079018, rs2489103092, rs2489103106, rs2489076726, rs2489076714, rs2489033738, rs2489039784, rs2129916804, rs2489104342, rs386833568, rs747058634, rs201333795, rs1554648113, rs759133707, rs775769857, rs1819058900, rs751822565, rs1313841674, rs2489008925, rs2489011374, rs386833545, rs2489036296, rs1401949733, rs2489076947, rs2489085309, rs1554648060, rs2489098058, rs1817122287, rs2489039902, rs2489078910, rs2489162390, rs772871471, rs2489104166, rs2489033590, rs2489110933, rs2489124595, rs2489124753, rs1587959976, rs2489102854, rs2489160744, rs121964974, rs121964976, rs386833549, rs121964977, rs121964979, rs121964980, rs1817626324, rs2489104177, rs2489011541, rs2489036333, rs2489160558, rs2489006052, rs749981093, rs2489033624, rs1817626453, rs1163159065, rs1426503452, rs1254300059, rs1587964981, rs2489110934, rs374968310, rs2489111109, rs2489124576, rs2489084081, rs2489106447, rs2489015973, rs1819724486, rs2489102759, rs2489162833, rs1563827503, rs2489016003, rs375447060, rs2489011352, rs1226098656, rs1818740811, rs2489106564, rs2130031785, rs2489033769, rs2489162816, rs2489006048, rs2489160608, rs2489110954, rs1818826951, rs2489162680, rs386833576, rs2489080171, rs758895400, rs191905539, rs768091555, rs1554643354, rs1554646710, rs1554643360, rs1554644678, rs1430968530, rs763517274, rs755313904, rs150171524, rs1554643619, rs1399754800, rs1554641505, rs749512886, rs1554641887, rs766762760, rs749882600, rs777365335, rs1554643370, rs750384225, rs769625871, rs1301895668, rs751025203, rs1286882965, rs10975674, rs1554648117, rs1554649675, rs978795483, rs1554652870, rs1259354298, rs373618804, rs772068893, rs774099283, rs767200188, rs386833559, rs1554641519, rs1429861000, rs1554646517, rs1554646529, rs1554646634, rs1554646653, rs1211616091, rs761957837, rs138484426, rs1251443902, rs1163356968, rs1477860542, rs1247180998, rs1563834980, rs1563864784, rs1296191006, rs386833542, rs1587951033, rs188269735, rs1587922096, rs386833535, rs1366947118, rs1345599468, rs151163582, rs762989914, rs386833575, rs386833516, rs386833517, rs386833518, rs386833519, rs386833520, rs386833521, rs386833522, rs386833523, rs386833524, rs386833526, rs386833528, rs386833531, rs386833532, rs386833534, rs386833536, rs386833537, rs386833538, rs386833539, rs386833540, rs386833541, rs386833543, rs386833546, rs386833547, rs121964975, rs386833550, rs386833552, rs386833553, rs386833554, rs386833557, rs386833558, rs386833560, rs386833563, rs386833564, rs386833567, rs386833569, rs386833570, rs386833573, rs386833574, rs386833577, rs386833579, rs386833580, rs386833581, rs386833582, rs386833585, rs386833586, rs386833587, rs386833588, rs386833589, rs386833590, rs386833591, rs386833572, rs1587908683, rs542056100, rs1587950355, rs765906340, rs1587958061, rs770743220, rs1251538998, rs1818691758, rs746124283, rs1819724531, rs1252460597, rs903653902, rs779434645, rs1818624667, rs267602258, rs1817555980, rs1817584930, rs1410625190, rs1449126451, rs1275684568, rs1818289368, rs1818316799, rs1818693456, rs1818312039, rs1817121202, rs759933539, rs1817123754, rs765893483, rs1817497939, rs149694787, rs1563836857, rs1818289122, rs1818289261, rs1038321056, rs1818404451, rs1818405533, rs1818407147, rs555359738, rs1818692381, rs143256976, rs1818695432, rs1818703974, rs776895767, rs1163351205, rs759699162, rs1819059889, rs1819702000	RCV001325842 RCV001638060 RCV003511751 RCV001360323 RCV001377475 RCV001379152 RCV001377093 RCV001387004 RCV001386717 RCV001387005 RCV001389070 RCV001389339 RCV001384194 RCV001389829 RCV001383294 RCV001388887 RCV001383644 RCV001389379 RCV001389728 RCV001385368 RCV001783380 RCV001782198 RCV002034263 RCV001923338 RCV002015099 RCV001989609 RCV002013532 RCV001959283 RCV001934250 RCV001984394 RCV001919165 RCV001907120 RCV001993654 RCV001939427 RCV001902855 RCV001999070 RCV001938480 RCV001961771 RCV002029780 RCV001880795 RCV001970112 RCV001992724 RCV001953700 RCV001953702 RCV001949673 RCV001946157 RCV002025734 RCV002007219 RCV001993102 RCV001994664 RCV001994724 RCV002022056 RCV001983671 RCV001920147 RCV001921693 RCV001994485 RCV002007582 RCV001994499 RCV002007624 RCV001999705 RCV002035503 RCV001994506 RCV002034925 RCV001941898 RCV001939557 RCV001939585 RCV001986682 RCV001941627 RCV001946893 RCV001946796 RCV001970223 RCV002001026 RCV001956185 RCV002000776 RCV002026185 RCV001967347 RCV001982119 RCV001975089 RCV001949627 RCV001980573 RCV001977308 RCV002001594 RCV001981249 RCV002249058 RCV002249059 RCV002306480 RCV002306537 RCV002306579 RCV002306584 RCV002306806 RCV002309755 RCV002309861 RCV002309867 RCV002309923 RCV002309966 RCV002310004 RCV002310039 RCV002307900 RCV002307907 RCV002308013 RCV002308256 RCV002308341 RCV002308355 RCV002309161 RCV002309305 RCV002309424 RCV002306845 RCV002306980 RCV002307121 RCV002307167 RCV002310419 RCV002308398 RCV002308419 RCV002308467 RCV003058211 RCV003062195 RCV003058212 RCV003058213 RCV003062198 RCV003073158 RCV003088245 RCV003085003 RCV002624851 RCV002578753 RCV002714950 RCV002690448 RCV002751326 RCV002800471 RCV002819297 RCV002819149 RCV002791451 RCV002791168 RCV002835370 RCV002871209 RCV002898769 RCV002889371 RCV002881255 RCV002880373 RCV002889684 RCV002867703 RCV002872660 RCV002895034 RCV000198720 RCV003009089 RCV003011655 RCV003009831 RCV003008476 RCV003029475 RCV003047565 RCV003040251 RCV003032967 RCV003123373 RCV000411816 RCV000012762 RCV000012765 RCV000012766 RCV000012767 RCV000012768 RCV000012769 RCV000012770 RCV003333657 RCV003335865 RCV003335898 RCV003512249 RCV003512299 RCV003512986 RCV003513604 RCV003513605 RCV003513606 RCV003513607 RCV003513609 RCV003513610 RCV003513611 RCV003513612 RCV003513613 RCV003513614 RCV003513615 RCV003513616 RCV003511657 RCV003511706 RCV003511717 RCV003511945 RCV003511964 RCV003512492 RCV003624554 RCV003624630 RCV003624687 RCV003625164 RCV003624893 RCV003625281 RCV003625348 RCV003625480 RCV003625288 RCV003625337 RCV003625380 RCV003625660 RCV003625860 RCV003625905 RCV003625936 RCV003623909 RCV003623940 RCV003624006 RCV003624336 RCV000412474 RCV003512048 RCV000499785 RCV000560119 RCV000537902 RCV000534696 RCV000526391 RCV000550531 RCV000586601 RCV000616020 RCV000666682 RCV000638271 RCV000638285 RCV000638272 RCV000670173 RCV000669902 RCV000670172 RCV000674862 RCV000673972 RCV000673967 RCV000670618 RCV000669887 RCV000670163 RCV005614436 RCV000670171 RCV000671712 RCV000674479 RCV000664632 RCV000670170 RCV000670145 RCV000670165 RCV000674678 RCV000666250 RCV000674197 RCV000671228 RCV000666921 RCV000670072 RCV000670154 RCV000674286 RCV000673215 RCV000670627 RCV000670162 RCV000671778 RCV000674186 RCV000671620 RCV000672824 RCV000669298 RCV000674854 RCV006265185 RCV000674732 RCV000667293 RCV000670325 RCV000672714 RCV000667354 RCV000669243 RCV000668297 RCV000704561 RCV000685534 RCV000707474 RCV000697307 RCV000704610 RCV000790373 RCV000792883 RCV000824302 RCV000815807 RCV000806344 RCV000814511 RCV000810838 RCV000805605 RCV000795305 RCV000797113 RCV000049444 RCV000049445 RCV000049446 RCV000049447 RCV000049448 RCV000049449 RCV000049450 RCV000049451 RCV000049452 RCV000049453 RCV000049454 RCV000049456 RCV000049459 RCV000049460 RCV000049462 RCV000049463 RCV000049464 RCV000049465 RCV000049466 RCV000049467 RCV000049468 RCV000049469 RCV000049470 RCV000049471 RCV000049473 RCV000049474 RCV000049475 RCV000049476 RCV000049478 RCV000049480 RCV000049481 RCV000049482 RCV000049485 RCV000049486 RCV000049487 RCV000049488 RCV000049491 RCV000049492 RCV000049495 RCV000049496 RCV000049497 RCV000049498 RCV000049500 RCV000049501 RCV000049502 RCV000049503 RCV000049504 RCV000049505 RCV000049506 RCV000049507 RCV000049508 RCV000049509 RCV000049510 RCV000049511 RCV000049512 RCV000049513 RCV000049514 RCV000049515 RCV000049516 RCV000049517 RCV000049583 RCV000985036 RCV000988140 RCV005093013 RCV000995554 RCV001004546 RCV001004547 RCV001068202 RCV001053812 RCV001042986 RCV001050271 RCV001042054 RCV001063324 RCV001060642 RCV001041567 RCV001052086 RCV001095655 RCV001095654 RCV003513608 RCV001196858 RCV001217184 RCV001216319 RCV001205237 RCV001204716 RCV001206860 RCV001223275 RCV001237271 RCV001238061 RCV001233386 RCV001226189 RCV001246746 RCV001263747 RCV001263748 RCV001263749 RCV001263750 RCV001263837 RCV001263838 RCV001263839 RCV001263840 RCV001263841 RCV001263842 RCV001263843 RCV001264010 RCV001264011 RCV001264012 RCV001264013 RCV001264014 RCV001264015 RCV001264016 RCV001264017 RCV001264342 RCV001264343 RCV001264344 RCV001264345 RCV001264346
Glycine encephalopathy 1	Likely pathogenic; Pathogenic	rs758575745, rs1447727878, rs1292183482, rs147951756, rs2129831647, rs1554643738, rs1817625926, rs1209943477, rs747853668, rs2489036171, rs2489076947, rs772871471, rs2489124701, rs2489098033, rs149070244, rs121964974, rs121964976, rs386833549, rs121964977, rs121964978, rs121964979, rs121964980, rs1226098656, rs191905539, rs1554646710, rs1554643360, rs1554644678, rs1430968530, rs763517274, rs150171524, rs1554641505, rs749512886, rs1288008254, rs1554641887, rs766762760, rs749882600, rs777365335, rs570097430, rs1554643370, rs750384225, rs769625871, rs1301895668, rs751025203, rs1286882965, rs10975674, rs1554648117, rs1554649675, rs978795483, rs1554652870, rs1554641737, rs1259354298, rs373618804, rs772068893, rs774099283, rs751822565, rs767200188, rs386833559, rs1554641519, rs1429861000, rs1196401015, rs1554646517, rs1554646529, rs1554646634, rs1554646653, rs1211616091, rs761957837, rs1207147043, rs138484426, rs1251443902, rs1163356968, rs1477860542, rs386833542, rs188269735, rs386833575, rs386833517, rs386833518, rs386833521, rs386833524, rs386833525, rs386833531, rs386833537, rs386833545, rs121964975, rs386833553, rs386833554, rs386833574, rs386833576, rs386833586, rs386833587, rs386833589, rs1587908683, rs770743220, rs1275684568, rs1818703974	RCV005040214 RCV005050368 RCV005630279 RCV005630280 RCV005630286 RCV005630287 RCV005042659 RCV005002716 RCV005042603 RCV005042799 RCV005603790 RCV005630322 RCV005630394 RCV005630421 RCV005003602 RCV004566730 RCV004566732 RCV004566733 RCV004566734 RCV004566735 RCV004566736 RCV004566737 RCV005047735 RCV005044608 RCV005044806 RCV005430549 RCV005430548 RCV005044807 RCV005049597 RCV005430375 RCV005430654 RCV004568533 RCV003989577 RCV005430817 RCV005430789 RCV005430788 RCV005430674 RCV005430639 RCV005430649 RCV005430695 RCV005430653 RCV005430708 RCV005046911 RCV005430388 RCV005430652 RCV005430645 RCV005430651 RCV004698510 RCV005430434 RCV005430797 RCV005430697 RCV005046865 RCV005430809 RCV005430643 RCV005430647 RCV005430803 RCV005430760 RCV005049646 RCV005430646 RCV005430648 RCV005046892 RCV005430795 RCV005430705 RCV005430627 RCV005430744 RCV005430622 RCV005430816 RCV005430437 RCV005004354 RCV005430560 RCV005046887 RCV005430741 RCV005430561 RCV005430620 RCV005430589 RCV005046964 RCV005004424 RCV005047064 RCV004566898 RCV005042153 RCV005042154 RCV005430473 RCV005049410 RCV005049411 RCV005867837 RCV005042157 RCV004566899 RCV005430474 RCV005042158 RCV005430475 RCV005430476 RCV005042159 RCV005430112 RCV005003444 RCV005430477 RCV003992429 RCV005225215 RCV005040030 RCV005633979 RCV005630378
Obesity	Pathogenic	rs121964976	RCV000449527
Retinitis pigmentosa	Likely pathogenic; Pathogenic	rs758575745	RCV004545214
Smith-Magenis Syndrome-like	Pathogenic	rs1114167353	RCV000491029

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Abnormal brain morphology	Conflicting classifications of pathogenicity	rs772574530	RCV000454245
Cervical cancer	Benign; Conflicting classifications of pathogenicity	rs145062104, rs77712643, rs144090917, rs140877566, rs535143891	RCV005922126 RCV005925313 RCV005893886 RCV005895138 RCV005900579
Cholangiocarcinoma	Benign	rs145062104	RCV005922129
Familial pancreatic carcinoma	Conflicting classifications of pathogenicity	rs150095531	RCV005900578
Gastric cancer	Benign	rs113067442	RCV005923078
Hepatocellular carcinoma	Likely benign; Conflicting classifications of pathogenicity; Benign	rs141980284, rs144090917, rs143119940	RCV005912878 RCV005893885 RCV005900572
Intellectual disability	Conflicting classifications of pathogenicity; Benign; Likely benign	rs141152043, rs144666843	RCV005625574 RCV005625575
Lung cancer	Benign	rs113067442, rs77712643	RCV005923079 RCV005925314
Malignant tumor of esophagus	Benign; Conflicting classifications of pathogenicity; Likely benign	rs145062104, rs140877566, rs143119940	RCV005922124 RCV005895137 RCV005900573
Nonpapillary renal cell carcinoma	Benign; Likely benign	rs145062104, rs143119940	RCV005922125 RCV005900574
Ovarian cancer	Conflicting classifications of pathogenicity	rs140877566, rs150095531	RCV005895139 RCV005900577
Ovarian serous cystadenocarcinoma	Likely benign; Benign; Conflicting classifications of pathogenicity	rs41281775, rs143119940, rs535143891	RCV005916210 RCV005900575 RCV005900580
Sarcoma	Likely benign; Benign; Conflicting classifications of pathogenicity	rs41281775, rs145062104, rs140877566	RCV005916209 RCV005922127 RCV005895140
See cases	Uncertain significance	rs149133229	RCV002252105
Thymoma	Benign	rs145062104	RCV005922128
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	rs143119940	RCV005900576
Uterine corpus endometrial carcinoma	Benign	rs145062104, rs77712643	RCV005922130 RCV005925315

Associations from Text Mining
Disease Name	Relationship Type	References
Anti N Methyl D Aspartate Receptor Encephalitis	Associate	31279534
Breast Neoplasms	Associate	25496516
Carcinogenesis	Associate	22225612
Carcinoma Ductal	Associate	25053597
Carcinoma Hepatocellular	Inhibit	30804330
Carcinoma Hepatocellular	Associate	35508111
Carcinoma Lobular	Associate	25053597
Carcinoma Non Small Cell Lung	Associate	22225612
Cerebral Infarction	Associate	26352407
Colorectal Neoplasms	Associate	25117815
Corticobasal Degeneration	Associate	28271184
Endometrial Neoplasms	Associate	31692912
Heredodegenerative Disorders Nervous System	Associate	32421718
Hyperglycinemia Nonketotic	Associate	17361008, 24334290, 26947380, 27362913, 28416785, 28737873, 29232014, 29304759, 31349202, 32421718
Hypertension Pulmonary	Associate	26352407
Lung Neoplasms	Associate	22225612
Neoplasm Metastasis	Associate	30575323, 37781511
Neoplasm Metastasis	Inhibit	30804330
Neoplasms	Associate	22225612, 24979213, 32055850, 35508111, 36275705
Neural Tube Defects	Associate	29232014
Neuroblastoma	Associate	37545226
Neurodegenerative Diseases	Associate	22121227
Osteosarcoma	Associate	29210060
Periodontitis	Associate	27531006
Primary hyperoxaluria type 1	Inhibit	31279534
Prostatic Neoplasms	Associate	37781511
Psychotic Disorders	Associate	31279534
Renal Insufficiency Chronic	Associate	26352407
Schizophrenia	Associate	29232014
Squamous Cell Carcinoma of Head and Neck	Associate	37245006
Supranuclear Palsy Progressive	Associate	28271184
Thyroid Neoplasms	Associate	27277113
Triple Negative Breast Neoplasms	Associate	24390667, 40217479