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	1491
Gene name	Cystathionine gamma-lyase
Gene symbol	CTH
Synonyms (NCBI Gene)	CGLCSE
Chromosome	1
Chromosome location	1p31.1
Summary	This gene encodes a cytoplasmic enzyme in the trans-sulfuration pathway that converts cystathione derived from methionine into cysteine. Glutathione synthesis in the liver is dependent upon the availability of cysteine. Mutations in this gene cause cystat

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28941785	C>A,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Genic upstream transcript variant, coding sequence variant, 5 prime UTR variant, missense variant
rs28941786	C>G,T	Pathogenic	Stop gained, coding sequence variant, missense variant
rs773107808	C>A,T	Likely-pathogenic	Stop gained, synonymous variant, coding sequence variant

Show/Hide all (65)

miRTarBase ID	miRNA	Experiments	Reference
MIRT019085	hsa-miR-335-5p	Microarray	18185580
MIRT024887	hsa-miR-215-5p	Microarray	19074876
MIRT026956	hsa-miR-192-5p	Microarray	19074876
MIRT030353	hsa-miR-26b-5p	Microarray	19088304
MIRT914677	hsa-miR-106a	CLIP-seq
MIRT914678	hsa-miR-106b	CLIP-seq
MIRT914679	hsa-miR-1193	CLIP-seq
MIRT914680	hsa-miR-1256	CLIP-seq
MIRT914681	hsa-miR-128	CLIP-seq
MIRT914682	hsa-miR-1299	CLIP-seq
MIRT914683	hsa-miR-150	CLIP-seq
MIRT914684	hsa-miR-15a	CLIP-seq
MIRT914685	hsa-miR-15b	CLIP-seq
MIRT914686	hsa-miR-16	CLIP-seq
MIRT914687	hsa-miR-17	CLIP-seq
MIRT914688	hsa-miR-195	CLIP-seq
MIRT914689	hsa-miR-1976	CLIP-seq
MIRT914690	hsa-miR-199a-3p	CLIP-seq
MIRT914691	hsa-miR-199b-3p	CLIP-seq
MIRT914692	hsa-miR-20a	CLIP-seq
MIRT914693	hsa-miR-20b	CLIP-seq
MIRT914694	hsa-miR-2392	CLIP-seq
MIRT914695	hsa-miR-27a	CLIP-seq
MIRT914696	hsa-miR-27b	CLIP-seq
MIRT914697	hsa-miR-302a	CLIP-seq
MIRT914698	hsa-miR-302b	CLIP-seq
MIRT914699	hsa-miR-302c	CLIP-seq
MIRT914700	hsa-miR-302d	CLIP-seq
MIRT914701	hsa-miR-302e	CLIP-seq
MIRT914702	hsa-miR-3129-5p	CLIP-seq
MIRT914703	hsa-miR-3199	CLIP-seq
MIRT914704	hsa-miR-372	CLIP-seq
MIRT914705	hsa-miR-373	CLIP-seq
MIRT914706	hsa-miR-424	CLIP-seq
MIRT914707	hsa-miR-4258	CLIP-seq
MIRT914708	hsa-miR-4269	CLIP-seq
MIRT914709	hsa-miR-4438	CLIP-seq
MIRT914710	hsa-miR-4454	CLIP-seq
MIRT914711	hsa-miR-4524	CLIP-seq
MIRT914712	hsa-miR-4660	CLIP-seq
MIRT914713	hsa-miR-4666-5p	CLIP-seq
MIRT914714	hsa-miR-4676-5p	CLIP-seq
MIRT914715	hsa-miR-4691-5p	CLIP-seq
MIRT914716	hsa-miR-4707-3p	CLIP-seq
MIRT914717	hsa-miR-4720-5p	CLIP-seq
MIRT914718	hsa-miR-4799-3p	CLIP-seq
MIRT914719	hsa-miR-497	CLIP-seq
MIRT914720	hsa-miR-503	CLIP-seq
MIRT914721	hsa-miR-5095	CLIP-seq
MIRT914722	hsa-miR-512-3p	CLIP-seq
MIRT914723	hsa-miR-513a-5p	CLIP-seq
MIRT914724	hsa-miR-519d	CLIP-seq
MIRT914725	hsa-miR-520a-3p	CLIP-seq
MIRT914726	hsa-miR-520b	CLIP-seq
MIRT914727	hsa-miR-520c-3p	CLIP-seq
MIRT914728	hsa-miR-520d-3p	CLIP-seq
MIRT914729	hsa-miR-520e	CLIP-seq
MIRT914730	hsa-miR-548t	CLIP-seq
MIRT914731	hsa-miR-562	CLIP-seq
MIRT914732	hsa-miR-575	CLIP-seq
MIRT914733	hsa-miR-576-5p	CLIP-seq
MIRT914734	hsa-miR-646	CLIP-seq
MIRT914735	hsa-miR-875-3p	CLIP-seq
MIRT914736	hsa-miR-93	CLIP-seq
MIRT914737	hsa-miR-936	CLIP-seq

Show/Hide all (40)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004123	Function	Cystathionine gamma-lyase activity	IBA
GO:0004123	Function	Cystathionine gamma-lyase activity	IDA	10212249, 19019829, 19428278
GO:0004123	Function	Cystathionine gamma-lyase activity	IEA
GO:0005515	Function	Protein binding	IPI	22169477, 25416956, 32296183
GO:0005516	Function	Calmodulin binding	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006534	Process	Cysteine metabolic process	TAS	1339280
GO:0006629	Process	Lipid metabolic process	IEA
GO:0008652	Process	Amino acid biosynthetic process	IEA
GO:0016829	Function	Lyase activity	IEA
GO:0018272	Process	Protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine	IDA	19019829
GO:0019343	Process	Cysteine biosynthetic process via cystathionine	IBA
GO:0019343	Process	Cysteine biosynthetic process via cystathionine	IDA	19428278
GO:0019344	Process	Cysteine biosynthetic process	IDA	10212249
GO:0019344	Process	Cysteine biosynthetic process	IEA
GO:0019346	Process	Transsulfuration	IBA
GO:0019346	Process	Transsulfuration	IDA	19428278
GO:0019346	Process	Transsulfuration	IEA
GO:0030170	Function	Pyridoxal phosphate binding	IBA
GO:0030170	Function	Pyridoxal phosphate binding	IDA	10212249, 19019829
GO:0030170	Function	Pyridoxal phosphate binding	IEA
GO:0030968	Process	Endoplasmic reticulum unfolded protein response	TAS	22169477
GO:0042802	Function	Identical protein binding	IPI	16189514, 25416956, 32296183
GO:0043066	Process	Negative regulation of apoptotic process	IEA
GO:0043123	Process	Positive regulation of canonical NF-kappaB signal transduction	IEA
GO:0044524	Process	Protein sulfhydration	IMP	22169477
GO:0044540	Function	L-cystine L-cysteine-lyase (deaminating)	IEA
GO:0044540	Function	L-cystine L-cysteine-lyase (deaminating)	IMP	22169477
GO:0047982	Function	Homocysteine desulfhydrase activity	IEA
GO:0051289	Process	Protein homotetramerization	IPI	19019829
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0070814	Process	Hydrogen sulfide biosynthetic process	IDA	19019829
GO:0070814	Process	Hydrogen sulfide biosynthetic process	TAS	19428278
GO:0080146	Function	L-cysteine desulfhydrase activity	IEA
GO:0098606	Function	Selenocystathionine gamma-lyase activity	IEA
GO:1904831	Process	Positive regulation of aortic smooth muscle cell differentiation	IMP	21659522
GO:1990830	Process	Cellular response to leukemia inhibitory factor	IEA
GO:2001234	Process	Negative regulation of apoptotic signaling pathway	IEA

MIM	HGNC	e!Ensembl
607657	2501	ENSG00000116761

P32929

Protein name

Cystathionine gamma-lyase (CGL) (CSE) (EC 4.4.1.1) (Cysteine desulfhydrase) (Cysteine-protein sulfhydrase) (Gamma-cystathionase) (Homocysteine desulfhydrase) (EC 4.4.1.2)

Protein function

Catalyzes the last step in the trans-sulfuration pathway from L-methionine to L-cysteine in a pyridoxal-5'-phosphate (PLP)-dependent manner, which consists on cleaving the L,L-cystathionine molecule into L-cysteine, ammonia and 2-oxobutanoate (P

PDB

2NMP , 3COG , 3ELP , 5EIG , 5TSU , 5TT2 , 6NBA , 6OVG

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01053	Cys_Met_Meta_PP	19 → 395	Cys/Met metabolism PLP-dependent enzyme	Domain

Tissue specificity

TISSUE SPECIFICITY: Highly expressed in liver (PubMed:10727430, PubMed:20305127). Also in muscle and lower expression in most tissues except heart, pituitary gland, spleen, thymus, and vascular tissue, where it is hardly detected (PubMed:20305127). {ECO:0

Sequence

MQEKDASSQGFLPHFQHFATQAIHVGQDPEQWTSRAVVPPISLSTTFKQGAPGQHSGFEY
SRSGNPTRNCLEKAVAALDGAKYCLAFASGLAATVTITHLLKAGDQIICMDDVYGGTNRY
FRQVASEFGLKISFVDCSKIKLLEAAITPETKLVWIETPTNPTQKVIDIEGCAHIVHKHG
DIILVVDNTFMSPYFQRPLALGADISMYSATKYMNGHSDVVMGLVSVNCESLHNRLRFLQ
NSLGAVPSPIDCYLCNRGLKTLHVRMEKHFKNGMAVAQFLESNPWVEKVIYPGLPSHPQH
ELVKRQCTGCTGMVTFYIKGTLQHAEIFLKNLKLFTLAESLGGFESLAELPAIMTHASVL
KNDRDVLGISDTLIRLSVGLEDEEDLLEDLDQALKAAHPPSGSHS

Sequence length

405

Interactions

View interactions

	KEGG		Reactome
	Glycine, serine and threonine metabolism Cysteine and methionine metabolism Selenocompound metabolism One carbon pool by folate Metabolic pathways Biosynthesis of amino acids		Degradation of cysteine and homocysteine Cysteine formation from homocysteine

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 (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Cystathioninuria	Likely pathogenic; Pathogenic	rs746818113, rs748374528, rs28941786, rs773107808	RCV001335877 RCV000003071 RCV000003074 RCV000490299	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (7)

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	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CTH-related disorder	Conflicting classifications of pathogenicity; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Homocysteine level elevated	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MELANOMA	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ULCERATIVE COLITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

CTH (cystathionine gamma-lyase)