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	2593
Gene name	Guanidinoacetate N-methyltransferase
Gene symbol	GAMT
Synonyms (NCBI Gene)	CCDS2HEL-S-20PIG2TP53I2
Chromosome	19
Chromosome location	19p13.3
Summary	The protein encoded by this gene is a methyltransferase that converts guanidoacetate to creatine, using S-adenosylmethionine as the methyl donor. Defects in this gene have been implicated in neurologic syndromes and muscular hypotonia, probably due to cre

Show/Hide all (28)

SNP ID	Visualize variation	Clinical significance	Consequence
rs80338734	C>A,G	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs80338735	C>T	Pathogenic	Coding sequence variant, synonymous variant
rs80338736	->GGCCCAGTCCCGG	Pathogenic	Coding sequence variant, frameshift variant
rs104894694	T>G	Pathogenic	Coding sequence variant, missense variant
rs121909272	C>T	Pathogenic	Coding sequence variant, missense variant
rs145817990	T>G	Likely-pathogenic	Missense variant, coding sequence variant
rs147739199	A>C,G	Likely-benign, conflicting-interpretations-of-pathogenicity, benign	Missense variant, genic downstream transcript variant, downstream transcript variant, coding sequence variant
rs200444143	C>A,T	Pathogenic	Missense variant, coding sequence variant, stop gained
rs200833152	A>G	Conflicting-interpretations-of-pathogenicity, not-provided, likely-benign	Missense variant, coding sequence variant
rs370421531	C>A,G,T	Pathogenic	Missense variant, coding sequence variant, stop gained
rs552210450	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs568392459	C>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Synonymous variant, coding sequence variant
rs570476209	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs747656257	G>A,T	Likely-pathogenic, uncertain-significance	Stop gained, coding sequence variant, missense variant
rs749390953	C>-,CC	Pathogenic	Frameshift variant, coding sequence variant
rs751099274	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs753198836	C>A,T	Likely-pathogenic	Coding sequence variant, missense variant
rs760101382	C>A,T	Pathogenic	Missense variant, coding sequence variant
rs779931959	->GAGGTGAGGTTGCAG	Likely-pathogenic, uncertain-significance	Coding sequence variant, inframe insertion
rs796052525	C>A,T	Likely-pathogenic	Missense variant, coding sequence variant, stop gained
rs886054247	A>T	Pathogenic	Missense variant, coding sequence variant
rs1057524499	T>A	Likely-pathogenic	Coding sequence variant, stop gained
rs1131691644	T>G	Pathogenic-likely-pathogenic	Coding sequence variant, missense variant
rs1131691930	T>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1369786965	G>A	Pathogenic	Stop gained, coding sequence variant
rs1384688313	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs1600158650	C>T	Likely-pathogenic	Splice acceptor variant
rs1600158894	C>G	Likely-pathogenic	Splice donor variant

Show/Hide all (71)

miRTarBase ID	miRNA	Experiments
MIRT1011709	hsa-miR-3545-3p	CLIP-seq
MIRT1011710	hsa-miR-3663-5p	CLIP-seq
MIRT1011711	hsa-miR-4496	CLIP-seq
MIRT1011712	hsa-miR-4635	CLIP-seq
MIRT1011713	hsa-miR-4680-5p	CLIP-seq
MIRT1011714	hsa-miR-651	CLIP-seq
MIRT2233184	hsa-miR-138	CLIP-seq
MIRT2233185	hsa-miR-3153	CLIP-seq
MIRT2233186	hsa-miR-320a	CLIP-seq
MIRT2233187	hsa-miR-320b	CLIP-seq
MIRT2233188	hsa-miR-320c	CLIP-seq
MIRT2233189	hsa-miR-320d	CLIP-seq
MIRT2233190	hsa-miR-4299	CLIP-seq
MIRT2233191	hsa-miR-4429	CLIP-seq
MIRT2233192	hsa-miR-642b	CLIP-seq
MIRT2536995	hsa-miR-1207-3p	CLIP-seq
MIRT2536996	hsa-miR-1273c	CLIP-seq
MIRT2233184	hsa-miR-138	CLIP-seq
MIRT2536997	hsa-miR-1915	CLIP-seq
MIRT2536998	hsa-miR-3683	CLIP-seq
MIRT2536999	hsa-miR-4446-3p	CLIP-seq
MIRT2537000	hsa-miR-4466	CLIP-seq
MIRT2537001	hsa-miR-4492	CLIP-seq
MIRT2537002	hsa-miR-4498	CLIP-seq
MIRT2537003	hsa-miR-450b-3p	CLIP-seq
MIRT2537004	hsa-miR-4519	CLIP-seq
MIRT2537005	hsa-miR-4685-5p	CLIP-seq
MIRT2537006	hsa-miR-4690-3p	CLIP-seq
MIRT2537007	hsa-miR-4713-3p	CLIP-seq
MIRT2537008	hsa-miR-4725-5p	CLIP-seq
MIRT2537009	hsa-miR-504	CLIP-seq
MIRT2537010	hsa-miR-548q	CLIP-seq
MIRT2537011	hsa-miR-638	CLIP-seq
MIRT2233192	hsa-miR-642b	CLIP-seq
MIRT2537012	hsa-miR-675	CLIP-seq
MIRT2537013	hsa-miR-762	CLIP-seq
MIRT2537014	hsa-miR-769-3p	CLIP-seq
MIRT2536995	hsa-miR-1207-3p	CLIP-seq
MIRT2536996	hsa-miR-1273c	CLIP-seq
MIRT2233184	hsa-miR-138	CLIP-seq
MIRT2536997	hsa-miR-1915	CLIP-seq
MIRT2681450	hsa-miR-3620	CLIP-seq
MIRT2536998	hsa-miR-3683	CLIP-seq
MIRT2681451	hsa-miR-3690	CLIP-seq
MIRT2681452	hsa-miR-378	CLIP-seq
MIRT2681453	hsa-miR-378b	CLIP-seq
MIRT2681454	hsa-miR-378c	CLIP-seq
MIRT2681455	hsa-miR-378d	CLIP-seq
MIRT2681456	hsa-miR-378e	CLIP-seq
MIRT2681457	hsa-miR-378f	CLIP-seq
MIRT2681458	hsa-miR-378h	CLIP-seq
MIRT2681459	hsa-miR-378i	CLIP-seq
MIRT2681460	hsa-miR-422a	CLIP-seq
MIRT2681461	hsa-miR-4308	CLIP-seq
MIRT2536999	hsa-miR-4446-3p	CLIP-seq
MIRT2537000	hsa-miR-4466	CLIP-seq
MIRT2537001	hsa-miR-4492	CLIP-seq
MIRT2537002	hsa-miR-4498	CLIP-seq
MIRT2537003	hsa-miR-450b-3p	CLIP-seq
MIRT2537004	hsa-miR-4519	CLIP-seq
MIRT2537005	hsa-miR-4685-5p	CLIP-seq
MIRT2537006	hsa-miR-4690-3p	CLIP-seq
MIRT2537007	hsa-miR-4713-3p	CLIP-seq
MIRT2537008	hsa-miR-4725-5p	CLIP-seq
MIRT2537009	hsa-miR-504	CLIP-seq
MIRT2537010	hsa-miR-548q	CLIP-seq
MIRT2537011	hsa-miR-638	CLIP-seq
MIRT2233192	hsa-miR-642b	CLIP-seq
MIRT2537012	hsa-miR-675	CLIP-seq
MIRT2537013	hsa-miR-762	CLIP-seq
MIRT2537014	hsa-miR-769-3p	CLIP-seq

Show/Hide all (21)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	28514442, 32296183, 33961781
GO:0005634	Component	Nucleus	IBA
GO:0005737	Component	Cytoplasm	IBA
GO:0005829	Component	Cytosol	TAS
GO:0006600	Process	Creatine metabolic process	TAS
GO:0006601	Process	Creatine biosynthetic process	IBA
GO:0006601	Process	Creatine biosynthetic process	IDA	8651275
GO:0006601	Process	Creatine biosynthetic process	IEA
GO:0006601	Process	Creatine biosynthetic process	IEA
GO:0006601	Process	Creatine biosynthetic process	TAS	9325156
GO:0006936	Process	Muscle contraction	TAS	8547310
GO:0007283	Process	Spermatogenesis	IEA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0008168	Function	Methyltransferase activity	TAS	9325156
GO:0009887	Process	Animal organ morphogenesis	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0030731	Function	Guanidinoacetate N-methyltransferase activity	IBA
GO:0030731	Function	Guanidinoacetate N-methyltransferase activity	IEA
GO:0030731	Function	Guanidinoacetate N-methyltransferase activity	IMP	8651275
GO:0032259	Process	Methylation	IEA
GO:0040014	Process	Regulation of multicellular organism growth	IEA

MIM	HGNC	e!Ensembl
601240	4136	ENSG00000130005

Q14353

Protein name

Guanidinoacetate N-methyltransferase (EC 2.1.1.2)

Protein function

Converts guanidinoacetate to creatine, using S-adenosylmethionine as the methyl donor (PubMed:24415674, PubMed:26003046, PubMed:26319512). Important in nervous system development (PubMed:24415674). {ECO:0000269|PubMed:24415674, ECO:0000269|PubMe

PDB

3ORH

Family and domains

Tissue specificity

TISSUE SPECIFICITY: Expressed in liver. {ECO:0000269|PubMed:8651275}.

Sequence

MSAPSATPIFAPGENCSPAWGAAPAAYDAADTHLRILGKPVMERWETPYMHALAAAASSK
GGRVLEVGFGMAIAASKVQEAPIDEHWIIECNDGVFQRLRDWAPRQTHKVIPLKGLWEDV
APTLPDGHFDGILYDTYPLSEETWHTHQFNFIKNHAFRLLKPGGVLTYCNLTSWGELMKS
KYSDITIMFEETQVPALLEAGFRRENIRTEVMALVPPADCRYYAFPQMITPLVTKG

Sequence length

236

Interactions

View interactions

	KEGG		Reactome
	Glycine, serine and threonine metabolism Arginine and proline metabolism Metabolic pathways		Creatine metabolism

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 (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the nervous system	Pathogenic	rs1369786965	RCV001814217	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cerebral creatine deficiency syndrome	Likely pathogenic; Pathogenic	rs2144636246, rs2144638033, rs2144640856, rs2144636856, rs2144637533, rs2144638048, rs2082622867, rs1215576338, rs2082632611, rs1569009071, rs80338734, rs745740974, rs1483148182, rs2144636455, rs2144640900 View all (69 more)	RCV001379333 RCV001377759 RCV001379555 RCV001390318 RCV001383246 View all (85 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Deficiency of guanidinoacetate methyltransferase	Likely pathogenic; Pathogenic	rs2144636246, rs2144638033, rs2144637533, rs2144638048, rs2082622867, rs1215576338, rs1569009071, rs80338734, rs2144640849, rs2144638078, rs2082632873, rs745740974, rs1483148182, rs2144636453, rs1600158570 View all (65 more)	RCV003298627 RCV003469631 RCV003462990 RCV003469721 RCV002504647 View all (82 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
GAMT-related disorder	Pathogenic; Likely pathogenic	rs865951519, rs370421531, rs1371496558, rs967689898	RCV003919013 RCV003907657 RCV003928960 RCV003413863	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability	Likely pathogenic	rs2082618808	RCV001251993	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Parkinson disease, late-onset	Pathogenic	rs761621516	RCV005235769	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (10)

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.
AMINO ACID METABOLISM, INBORN ERRORS	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CEREBRAL CREATINE DEFICIENCY SYNDROME 2	—	HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL NEUROLOGIC ANOMALIES	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CREATINE DEFICIENCY SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Guanidinoacetate methyltransferase (GAMT) deficiency	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MENTAL RETARDATION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SEIZURES	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (38)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Amino Acid Metabolism, Inborn Errors	Disorder of amino acid metabolism	CTD_human_DG	15651030		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Amino Acid Metabolism, Inherited Disorders	Inherited Errors of Amino Acid Metabolism	CTD_human_DG	15651030		★★★★★ ★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Clonic Seizures	Clonic Seizures	CTD_human_DG	15651030		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colonic Neoplasms	Colonic neoplasm	Pubtator	35712285	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Complex partial seizure with impairment of consciousness	Dyscognitive seizures	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Complex partial seizures	Seizure	CTD_human_DG	15651030		★★★★★ ★☆☆☆☆ Found in Text Mining only
Complex partial seizures	Seizure	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Creatine deficiency, X-linked	Creatine deficiency	BEFREE	25192512		★★★★★ ★☆☆☆☆ Found in Text Mining only
Creatine deficiency, X-linked	Creatine deficiency	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Epileptic drop attack	Hypotonic seizures	CTD_human_DG	15651030		★★★★★ ★☆☆☆☆ Found in Text Mining only
Epileptic drop attack	Hypotonic seizures	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Generalized myoclonic seizures	Myoclonic Seizures	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Generalized seizures	Seizure	CTD_human_DG	15651030		★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Guanidinoacetate methyltransferase deficiency	Guanidinoacetate Methyltransferase Deficiency	CLINVAR_DG	11136556, 11978605, 12557293, 15108290, 15651030, 16169544, 16855203, 17171576, 17336114, 19027335, 23583224, 23660394, 24071436, 24268530, 24415674, 8651275 View all (1 more)		★★★★★ ★☆☆☆☆ Found in Text Mining only
Guanidinoacetate methyltransferase deficiency	Guanidinoacetate Methyltransferase Deficiency	CLINGEN_DG	11136556, 12557293, 12701824, 13192118, 15028668, 15108290, 16293431, 16899382, 17466557, 17789505, 24415674, 28808834, 8473283, 8651275		★★★★★ ★☆☆☆☆ Found in Text Mining only
Guanidinoacetate methyltransferase deficiency	Guanidinoacetate Methyltransferase Deficiency	UNIPROT_DG	12468279, 15108290, 15651030, 16293431, 16855203, 17101918, 17466557, 19388150, 23660394, 24415674, 8651275		★★★★★ ★☆☆☆☆ Found in Text Mining only
Guanidinoacetate methyltransferase deficiency	Guanidinoacetate Methyltransferase Deficiency	CTD_human_DG	15651030		★★★★★ ★☆☆☆☆ Found in Text Mining only
Guanidinoacetate methyltransferase deficiency	Guanidinoacetate Methyltransferase Deficiency	BEFREE	16899382, 24415674, 26003046, 26319512		★★★★★ ★☆☆☆☆ Found in Text Mining only
Guanidinoacetate methyltransferase deficiency	Guanidinoacetate Methyltransferase Deficiency	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Guanidinoacetate methyltransferase deficiency	Guanidinoacetate Methyltransferase Deficiency	GENOMICS_ENGLAND_DG	24268530, 8651275		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	CTD_human_DG	15651030		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	8651275		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Jacksonian Seizure	Jacksonian Seizure	CTD_human_DG	15651030		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malnutrition	Malnutrition	BEFREE	15028668		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mental deficiency	Mental retardation	CTD_human_DG	15651030		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	23880140		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	38297362	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Profound Mental Retardation	Mental retardation	CTD_human_DG	15651030		★★★★★ ★☆☆☆☆ Found in Text Mining only
Severe intellectual disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Single Seizure	Seizure	CTD_human_DG	15651030		★★★★★ ★☆☆☆☆ Found in Text Mining only
Speech Delay	Speech Delay	BEFREE	31222513		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	36790659	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Tonic - clonic seizures	Seizure	CTD_human_DG	15651030		★★★★★ ★☆☆☆☆ Found in Text Mining only
Tonic - clonic seizures	Seizure	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Visual seizure	Seizure	CTD_human_DG	15651030		★★★★★ ★☆☆☆☆ Found in Text Mining only

GAMT (guanidinoacetate N-methyltransferase)