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	2628
Gene name	Glycine amidinotransferase
Gene symbol	GATM
Synonyms (NCBI Gene)	AGATATCCDS3FRTSFRTS1RFS
Chromosome	15
Chromosome location	15q21.1
Summary	This gene encodes a mitochondrial enzyme that belongs to the amidinotransferase family. This enzyme is involved in creatine biosynthesis, whereby it catalyzes the transfer of a guanido group from L-arginine to glycine, resulting in guanidinoacetic acid, t

Show/Hide all (10)

SNP ID	Visualize variation	Clinical significance	Consequence
rs1346268	T>A,C,G	Drug-response	Genic upstream transcript variant, intron variant
rs80338737	C>A,T	Pathogenic	Missense variant, coding sequence variant, stop gained
rs80338738	C>A	Pathogenic	Splice donor variant
rs148564534	G>A	Benign, likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs151231277	A>G	Benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs397514708	G>A	Pathogenic	Coding sequence variant, stop gained
rs397514709	T>G	Pathogenic	Coding sequence variant, missense variant
rs397515542	->T	Pathogenic	Coding sequence variant, frameshift variant
rs775933965	G>A	Pathogenic	Coding sequence variant, stop gained
rs1566842679	C>T	Pathogenic	Coding sequence variant, 5 prime UTR variant, stop gained

Show/Hide all (56)

miRTarBase ID	miRNA	Experiments	Reference
MIRT021061	hsa-miR-155-5p	Reporter assay;Other	20584899
MIRT021061	hsa-miR-155-5p	Reporter assay;Other	18668040
MIRT024805	hsa-miR-215-5p	Microarray	19074876
MIRT026928	hsa-miR-192-5p	Microarray	19074876
MIRT657944	hsa-miR-3184-3p	HITS-CLIP	23824327
MIRT657943	hsa-miR-1264	HITS-CLIP	23824327
MIRT657942	hsa-miR-6845-3p	HITS-CLIP	23824327
MIRT657941	hsa-miR-567	HITS-CLIP	23824327
MIRT657940	hsa-miR-6830-3p	HITS-CLIP	23824327
MIRT657939	hsa-miR-6873-3p	HITS-CLIP	23824327
MIRT657938	hsa-miR-297	HITS-CLIP	23824327
MIRT657937	hsa-miR-4263	HITS-CLIP	23824327
MIRT657936	hsa-miR-4768-5p	HITS-CLIP	23824327
MIRT657935	hsa-miR-6833-3p	HITS-CLIP	23824327
MIRT657934	hsa-miR-6809-3p	HITS-CLIP	23824327
MIRT657944	hsa-miR-3184-3p	HITS-CLIP	23824327
MIRT657943	hsa-miR-1264	HITS-CLIP	23824327
MIRT657942	hsa-miR-6845-3p	HITS-CLIP	23824327
MIRT657941	hsa-miR-567	HITS-CLIP	23824327
MIRT657940	hsa-miR-6830-3p	HITS-CLIP	23824327
MIRT657939	hsa-miR-6873-3p	HITS-CLIP	23824327
MIRT657938	hsa-miR-297	HITS-CLIP	23824327
MIRT657937	hsa-miR-4263	HITS-CLIP	23824327
MIRT657936	hsa-miR-4768-5p	HITS-CLIP	23824327
MIRT657935	hsa-miR-6833-3p	HITS-CLIP	23824327
MIRT657934	hsa-miR-6809-3p	HITS-CLIP	23824327
MIRT1013521	hsa-let-7a	CLIP-seq
MIRT1013522	hsa-let-7b	CLIP-seq
MIRT1013523	hsa-let-7c	CLIP-seq
MIRT1013524	hsa-let-7d	CLIP-seq
MIRT1013525	hsa-let-7e	CLIP-seq
MIRT1013526	hsa-let-7f	CLIP-seq
MIRT1013527	hsa-let-7g	CLIP-seq
MIRT1013528	hsa-let-7i	CLIP-seq
MIRT1013529	hsa-miR-181a	CLIP-seq
MIRT1013530	hsa-miR-181b	CLIP-seq
MIRT1013531	hsa-miR-181c	CLIP-seq
MIRT1013532	hsa-miR-181d	CLIP-seq
MIRT1013533	hsa-miR-202	CLIP-seq
MIRT1013534	hsa-miR-203	CLIP-seq
MIRT1013535	hsa-miR-3148	CLIP-seq
MIRT1013536	hsa-miR-3171	CLIP-seq
MIRT1013537	hsa-miR-3647-3p	CLIP-seq
MIRT1013538	hsa-miR-3688-3p	CLIP-seq
MIRT1013539	hsa-miR-4262	CLIP-seq
MIRT1013540	hsa-miR-4282	CLIP-seq
MIRT1013541	hsa-miR-4426	CLIP-seq
MIRT1013542	hsa-miR-4647	CLIP-seq
MIRT1013543	hsa-miR-4662b	CLIP-seq
MIRT1013544	hsa-miR-490-5p	CLIP-seq
MIRT1013545	hsa-miR-543	CLIP-seq
MIRT1013546	hsa-miR-548ae	CLIP-seq
MIRT1013547	hsa-miR-548aj	CLIP-seq
MIRT1013548	hsa-miR-548am	CLIP-seq
MIRT1013549	hsa-miR-548x	CLIP-seq
MIRT1013550	hsa-miR-98	CLIP-seq

Show/Hide all (25)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IEA
GO:0005743	Component	Mitochondrial inner membrane	IEA
GO:0005758	Component	Mitochondrial intermembrane space	IBA
GO:0005758	Component	Mitochondrial intermembrane space	IDA	9218780
GO:0005758	Component	Mitochondrial intermembrane space	TAS
GO:0006600	Process	Creatine metabolic process	IMP	26490222
GO:0006601	Process	Creatine biosynthetic process	IBA
GO:0006601	Process	Creatine biosynthetic process	IDA	9218780
GO:0006601	Process	Creatine biosynthetic process	IEA
GO:0007611	Process	Learning or memory	IMP	26490222
GO:0014889	Process	Muscle atrophy	IMP	26490222
GO:0015067	Function	Amidinotransferase activity	IDA	36543883
GO:0015067	Function	Amidinotransferase activity	IEA
GO:0015068	Function	Glycine amidinotransferase activity	IBA
GO:0015068	Function	Glycine amidinotransferase activity	IDA	9218780, 27233232
GO:0015068	Function	Glycine amidinotransferase activity	IEA
GO:0016020	Component	Membrane	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0070062	Component	Extracellular exosome	HDA	23533145
GO:0120162	Process	Positive regulation of cold-induced thermogenesis	IEA
GO:0120162	Process	Positive regulation of cold-induced thermogenesis	ISS	28844881

MIM	HGNC	e!Ensembl
602360	4175	ENSG00000171766

P50440

Protein name

Glycine amidinotransferase, mitochondrial (EC 2.1.4.1) (L-arginine:glycine amidinotransferase) (Transamidinase)

Protein function

Transamidinase that catalyzes the transfer of the amidino group of L-arginine onto the amino moiety of acceptor metabolites such as glycine, beta-alanine, gamma-aminobutyric acid (GABA) and taurine yielding the corresponding guanidine derivative

PDB

1JDW , 1JDX , 2JDW , 2JDX , 3JDW , 4JDW , 5JDW , 6JDW , 7JDW , 8JDW , 9JDW

Family and domains

Tissue specificity

TISSUE SPECIFICITY: Expressed in brain, heart, kidney, liver, lung, salivary gland and skeletal muscle tissue, with the highest expression in kidney. Biallelically expressed in placenta and fetal tissues. {ECO:0000269|PubMed:16125225, ECO:0000269|PubMed:1

Sequence

MLRVRCLRGGSRGAEAVHYIGSRLGRTLTGWVQRTFQSTQAATASSRNSCAADDKATEPL
PKDCPVSSYNEWDPLEEVIVGRAENACVPPFTIEVKANTYEKYWPFYQKQGGHYFPKDHL
KKAVAEIEEMCNILKTEGVTVRRPDPIDWSLKYKTPDFESTGLYSAMPRDILIVVGNEII
EAPMAWRSRFFEYRAYRSIIKDYFHRGAKWTTAPKPTMADELYNQDYPIHSVEDRHKLAA
QGKFVTTEFEPCFDAADFIRAGRDIFAQRSQVTNYLGIEWMRRHLAPDYRVHIISFKDPN
PMHIDATFNIIGPGIVLSNPDRPCHQIDLFKKAGWTIITPPTPIIPDDHPLWMSSKWLSM
NVLMLDEKRVMVDANEVPIQKMFEKLGITTIKVNIRNANSLGGGFHCWTCDVRRRGTLQS
YLD

Sequence length

423

Interactions

View interactions

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

601

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Arginine:glycine amidinotransferase deficiency	Likely pathogenic; Pathogenic	rs2140644920, rs2140646735, rs2140641896, rs775933965, rs1217229880, rs80338737, rs1889477819, rs1461653218, rs2542005145, rs2542006088, rs2541986290, rs2541984266, rs2541989303, rs2541994594, rs2542009946 View all (12 more)	RCV002019076 RCV001946847 RCV001884143 RCV002305458 RCV002828399 RCV000007725 RCV003159284 RCV003159285 RCV003507657 RCV003508168 RCV003508170 RCV003506929 RCV003507013 RCV003507217 RCV003618294 RCV003618750 RCV003617338 RCV003617372 RCV003617436 RCV003859853 RCV000020462 RCV000694186 RCV001779072 RCV000049331 RCV000049332 RCV000049334 RCV001228102
Fanconi renotubular syndrome 1	Likely pathogenic; Pathogenic	rs2140657166, rs1325460408, rs80338738, rs397514708, rs1889443535	RCV001843325 RCV002279784 RCV005007885 RCV002490622 RCV001174509

Show/Hide Unknown Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Familial cancer of breast	Likely benign	rs368314780	RCV005926325
GATM-related disorder	Likely benign; Benign; Uncertain significance	rs766041671, rs151231277, rs550159982, rs768118194, rs2541981228, rs3210026, rs1595483270, rs750228246	RCV003928864 RCV004751275 RCV003935189 RCV003407686 RCV003406096 RCV003416807 RCV003406076 RCV003932559
Intellectual disability	Benign; Likely benign	rs148564534, rs1889641277	RCV001251999 RCV001251998
Lennox-Gastaut syndrome	Uncertain significance	rs1566840902	RCV000678800
Melanoma	Uncertain significance	rs368974196	RCV005893390
Ovarian serous cystadenocarcinoma	Likely benign	rs114512053	RCV005917583
Seizure	Conflicting classifications of pathogenicity	rs780777061	RCV000678799

Show/Hide Text Mining Associations (32)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Aortic Aneurysm Abdominal	Associate	22797469
Arginine Glycine Amidinotransferase Deficiency	Associate	11555793, 32883247
Autistic Disorder	Associate	28758966
Carcinoma Pancreatic Ductal	Associate	36319832
Carcinoma Renal Cell	Stimulate	25888189
Carcinoma Squamous Cell	Associate	34301206
Cerebral Hemorrhage	Inhibit	33461409
Creatine deficiency X linked	Associate	11555793, 23234264, 28758966, 38104212, 38452609
Creatine deficiency X linked	Stimulate	40338959
Diabetic Nephropathies	Associate	39838413
Fanconi Syndrome	Associate	36148635, 37286521
Fibromyalgia	Associate	32083545
Glioblastoma	Associate	36838582
Guanidinoacetate methyltransferase deficiency	Associate	39402976
Immune System Diseases	Associate	32083545
Kidney Diseases	Associate	34071541
Kidney Failure Chronic	Associate	36148635
Leukemia Myeloid Acute	Associate	34635505
Mental Disorders	Associate	32083545
Muscular Diseases	Associate	23995691, 24315367
Musculoskeletal Diseases	Associate	32083545
Myotoxicity	Associate	23995691, 29950617
Nervous System Diseases	Associate	11555793
Neurotoxicity Syndromes	Associate	38104212
Placenta Diseases	Associate	31991880
Pre Eclampsia	Stimulate	31991880
Prostate Cancer Hereditary 7	Associate	21965145
Prostatic Neoplasms	Associate	21965145
Prostatitis	Associate	21965145
Renal Insufficiency	Associate	36148635
Renal Insufficiency Chronic	Associate	19430482, 33783510, 34071541, 39284843
Tyrosine Kinase 2 Deficiency	Stimulate	34635505

GATM (glycine amidinotransferase)