MLYCD (malonyl-CoA decarboxylase)

Gene

• Entrez ID: 23417
• Gene name: Malonyl-CoA decarboxylase
• Gene symbol: MLYCD
• Synonyms (NCBI Gene): MCD
• Chromosome: 16
• Chromosome location: 16q23.3
• Summary: The product of this gene catalyzes the breakdown of malonyl-CoA to acetyl-CoA and carbon dioxide. Malonyl-CoA is an intermediate in fatty acid biosynthesis, and also inhibits the transport of fatty acyl CoAs into mitochondria. Consequently, the encoded pr

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs28937908	T>C	Pathogenic	Missense variant, coding sequence variant
rs104894528	C>G	Pathogenic	Coding sequence variant, stop gained
rs121908081	G>A	Pathogenic	Coding sequence variant, missense variant
rs138675420	G>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Synonymous variant, coding sequence variant, missense variant
rs201973830	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs374073138	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs398124254	->TGAAGC	Pathogenic	Coding sequence variant, inframe insertion
rs761146008	A>G	Pathogenic	Intron variant
rs796051991	G>-	Pathogenic, uncertain-significance	Coding sequence variant, frameshift variant
rs962135951	C>A,T	Pathogenic	Coding sequence variant, stop gained, missense variant
rs1064794623	A>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1294168838	GAGT>-	Pathogenic	Splice donor variant, coding sequence variant
rs1567636915	TT>-	Pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT017783	hsa-miR-335-5p	Microarray	18185580
MIRT1152672	hsa-miR-1200	CLIP-seq
MIRT1152673	hsa-miR-1203	CLIP-seq
MIRT1152674	hsa-miR-1228	CLIP-seq
MIRT1152675	hsa-miR-1273e	CLIP-seq
MIRT1152676	hsa-miR-1304	CLIP-seq
MIRT1152677	hsa-miR-140-3p	CLIP-seq
MIRT1152678	hsa-miR-1915	CLIP-seq
MIRT1152679	hsa-miR-19a	CLIP-seq
MIRT1152680	hsa-miR-19b	CLIP-seq
MIRT1152681	hsa-miR-2116	CLIP-seq
MIRT1152682	hsa-miR-2467-3p	CLIP-seq
MIRT1152683	hsa-miR-3119	CLIP-seq
MIRT1152684	hsa-miR-3126-5p	CLIP-seq
MIRT1152685	hsa-miR-3140-5p	CLIP-seq
MIRT1152686	hsa-miR-320a	CLIP-seq
MIRT1152687	hsa-miR-320b	CLIP-seq
MIRT1152688	hsa-miR-320c	CLIP-seq
MIRT1152689	hsa-miR-320d	CLIP-seq
MIRT1152690	hsa-miR-329	CLIP-seq
MIRT1152691	hsa-miR-3611	CLIP-seq
MIRT1152692	hsa-miR-362-3p	CLIP-seq
MIRT1152693	hsa-miR-3977	CLIP-seq
MIRT1152694	hsa-miR-3978	CLIP-seq
MIRT1152695	hsa-miR-431	CLIP-seq
MIRT1152696	hsa-miR-4318	CLIP-seq
MIRT1152697	hsa-miR-4325	CLIP-seq
MIRT1152698	hsa-miR-4419a	CLIP-seq
MIRT1152699	hsa-miR-4429	CLIP-seq
MIRT1152700	hsa-miR-4510	CLIP-seq
MIRT1152701	hsa-miR-4670-3p	CLIP-seq
MIRT1152702	hsa-miR-4677-5p	CLIP-seq
MIRT1152703	hsa-miR-4693-5p	CLIP-seq
MIRT1152704	hsa-miR-4699-5p	CLIP-seq
MIRT1152705	hsa-miR-4710	CLIP-seq
MIRT1152706	hsa-miR-4719	CLIP-seq
MIRT1152707	hsa-miR-4734	CLIP-seq
MIRT1152708	hsa-miR-485-5p	CLIP-seq
MIRT1152709	hsa-miR-516a-3p	CLIP-seq
MIRT1152710	hsa-miR-604	CLIP-seq
MIRT1152711	hsa-miR-892a	CLIP-seq
MIRT1152673	hsa-miR-1203	CLIP-seq
MIRT2043627	hsa-miR-129-3p	CLIP-seq
MIRT2043628	hsa-miR-1972	CLIP-seq
MIRT2043629	hsa-miR-2355-3p	CLIP-seq
MIRT2043630	hsa-miR-3120-3p	CLIP-seq
MIRT2043631	hsa-miR-33a	CLIP-seq
MIRT2043632	hsa-miR-33b	CLIP-seq
MIRT2043633	hsa-miR-4270	CLIP-seq
MIRT2043634	hsa-miR-4280	CLIP-seq
MIRT2043635	hsa-miR-4441	CLIP-seq
MIRT2043636	hsa-miR-4646-3p	CLIP-seq
MIRT2043637	hsa-miR-4646-5p	CLIP-seq
MIRT1152705	hsa-miR-4710	CLIP-seq
MIRT2043638	hsa-miR-4747-5p	CLIP-seq
MIRT2043639	hsa-miR-4755-3p	CLIP-seq
MIRT2043640	hsa-miR-4792	CLIP-seq
MIRT2043641	hsa-miR-642a	CLIP-seq
MIRT2043642	hsa-miR-891a	CLIP-seq
MIRT2273061	hsa-miR-1207-5p	CLIP-seq
MIRT2273062	hsa-miR-1226	CLIP-seq
MIRT1152674	hsa-miR-1228	CLIP-seq
MIRT1152677	hsa-miR-140-3p	CLIP-seq
MIRT1152679	hsa-miR-19a	CLIP-seq
MIRT1152680	hsa-miR-19b	CLIP-seq
MIRT1152682	hsa-miR-2467-3p	CLIP-seq
MIRT2273063	hsa-miR-29a	CLIP-seq
MIRT2273064	hsa-miR-29b	CLIP-seq
MIRT2273065	hsa-miR-29c	CLIP-seq
MIRT2273066	hsa-miR-3065-3p	CLIP-seq
MIRT1152690	hsa-miR-329	CLIP-seq
MIRT1152692	hsa-miR-362-3p	CLIP-seq
MIRT2273067	hsa-miR-3941	CLIP-seq
MIRT2043633	hsa-miR-4270	CLIP-seq
MIRT2043635	hsa-miR-4441	CLIP-seq
MIRT1152706	hsa-miR-4719	CLIP-seq
MIRT2273068	hsa-miR-4729	CLIP-seq
MIRT2273069	hsa-miR-4763-3p	CLIP-seq
MIRT2273070	hsa-miR-485-3p	CLIP-seq
MIRT1152708	hsa-miR-485-5p	CLIP-seq
MIRT2273071	hsa-miR-603	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
PPARA	Unknown	16434556
PPARGC1A	Unknown	16434556

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002931	Process	Response to ischemia	IEA
GO:0002931	Process	Response to ischemia	ISS
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005737	Component	Cytoplasm	IDA	10455107
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IDA	10417274
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	IBA
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0005759	Component	Mitochondrial matrix	ISS
GO:0005777	Component	Peroxisome	IDA	10417274, 10455107
GO:0005777	Component	Peroxisome	IEA
GO:0005782	Component	Peroxisomal matrix	IBA
GO:0005782	Component	Peroxisomal matrix	IEA
GO:0005782	Component	Peroxisomal matrix	ISS
GO:0005782	Component	Peroxisomal matrix	TAS
GO:0005829	Component	Cytosol	TAS
GO:0006085	Process	Acetyl-CoA biosynthetic process	IBA
GO:0006085	Process	Acetyl-CoA biosynthetic process	IDA	9869665, 10417274, 10455107
GO:0006085	Process	Acetyl-CoA biosynthetic process	IEA
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006631	Process	Fatty acid metabolic process	IEA
GO:0006633	Process	Fatty acid biosynthetic process	IBA
GO:0006633	Process	Fatty acid biosynthetic process	IDA	15003260
GO:0006633	Process	Fatty acid biosynthetic process	IEA
GO:0006637	Process	Acyl-CoA metabolic process	IEA
GO:0006637	Process	Acyl-CoA metabolic process	TAS
GO:0007584	Process	Response to nutrient	IEA
GO:0010906	Process	Regulation of glucose metabolic process	IEA
GO:0010906	Process	Regulation of glucose metabolic process	IMP	18314420
GO:0016829	Function	Lyase activity	IEA
GO:0016831	Function	Carboxy-lyase activity	IEA
GO:0019395	Process	Fatty acid oxidation	IEA
GO:0031998	Process	Regulation of fatty acid beta-oxidation	IEA
GO:0042802	Function	Identical protein binding	IPI	23791943
GO:0046320	Process	Regulation of fatty acid oxidation	IEA
GO:0046321	Process	Positive regulation of fatty acid oxidation	IEA
GO:0046321	Process	Positive regulation of fatty acid oxidation	IMP	18314420
GO:0050080	Function	Malonyl-CoA decarboxylase activity	EXP	10455107
GO:0050080	Function	Malonyl-CoA decarboxylase activity	IBA
GO:0050080	Function	Malonyl-CoA decarboxylase activity	IDA	9869665, 10417274, 10455107, 15003260
GO:0050080	Function	Malonyl-CoA decarboxylase activity	IEA
GO:2001294	Process	Malonyl-CoA catabolic process	IBA
GO:2001294	Process	Malonyl-CoA catabolic process	IDA	10417274, 10455107, 15003260
GO:2001294	Process	Malonyl-CoA catabolic process	IEA

Other IDs

• MIM: 606761
• HGNC: 7150
• e!Ensembl: ENSG00000103150

Protein

• UniProt ID: O95822
• Protein name: Malonyl-CoA decarboxylase, mitochondrial (MCD) (EC 4.1.1.9)
• Protein function: Catalyzes the conversion of malonyl-CoA to acetyl-CoA. In the fatty acid biosynthesis MCD selectively removes malonyl-CoA and thus assures that methyl-malonyl-CoA is the only chain elongating substrate for fatty acid synthase and that fatty acid
• PDB: 2YGW, 4F0X
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF17408	MCD_N	95 → 190	Malonyl-CoA decarboxylase N-terminal domain	Domain
  PF05292	MCD	193 → 457	Malonyl-CoA decarboxylase C-terminal domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Expressed in fibroblasts and hepatoblastoma cells (at protein level). Expressed strongly in heart, liver, skeletal muscle, kidney and pancreas. Expressed in myotubes. Expressed weakly in brain, placenta, spleen, thymus, testis, ovary a
• Sequence:

  MRGFGPGLTARRLLPLRLPPRPPGPRLASGQAAGALERAMDELLRRAVPPTPAYELREKT
  PAPAEGQCADFVSFYGGLAETAQRAELLGRLARGFGVDHGQVAEQSAGVLHLRQQQREAA
  VLLQAEDRLRYALVPRYRGLFHHISKLDGGVRFLVQLRADLLEAQALKLVEGPDVREMNG
  VLKGMLSEWFSSGFLNLERVTWHSPCEVLQKISEAEAVHPVKNWMDMKRRVGPYRRCYFF
  SHCSTPGEPLVVLHVALTGDISSNIQAIVKEHPPSETEEKNKITAAIFYSISLTQQGLQG
  VELGTFLIKRVVKELQREFPHLGVFSSLSPIPGFTKWLLGLLNSQTKEHGRNELFTDSEC
  KEISEITGGPINETLKLLLSSSEWVQSEKLVRALQTPLMRLCAWYLYGEKHRGYALNPVA
  NFHLQNGAVLWRINWMADVSLRGITGSCGLMANYRYFLEETGPNSTSYLGSKIIKASEQV
  LSLVAQFQKNSKL

• Sequence length: 493

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Deficiency of malonyl-CoA decarboxylase	Pathogenic; Likely pathogenic	rs2151057083, rs1906699127, rs757983774, rs1375748581, rs759043861, rs760768992, rs987846203, rs938617354, rs2507370774, rs775425515, rs777414552, rs750150415, rs104894528, rs761146008, rs1294168838, rs1567636915, rs28937908, rs1177558417, rs796051991, rs2507371773, rs2507380738, rs1179555424, rs1324491526, rs2507380841, rs2507370822, rs2507380620, rs2507387607, rs1906688548, rs201963260, rs2507370941, rs528074239, rs2507370766, rs2507382113, rs1597286264, rs1907006410, rs2507391940, rs2507380638, rs2507382391, rs2507371212, rs2507387531, rs2507382189, rs1464925145, rs1243469712, rs1906697955, rs2507382260, rs755172155, rs768903353, rs2507382078, rs1907006084, rs1906687546	RCV001382913 RCV001783642 RCV001783643 RCV003608982 RCV003147673 RCV001890786 RCV001921529 RCV001896582 RCV002470523 RCV003064359 RCV003058509 RCV002584930 RCV000004270 RCV000004271 RCV000004272 RCV000004273 RCV000004275 RCV000004276 RCV000778481 RCV002726200 RCV002834860 RCV003778276 RCV003503586 RCV003502830 RCV003503819 RCV003502433 RCV003502466 RCV003504031 RCV003503970 RCV003503265 RCV003503279 RCV003610313 RCV003610398 RCV003610340 RCV003608717 RCV003608710 RCV003608857 RCV003608878 RCV003608904 RCV003608866 RCV003610583 RCV003610699 RCV003610791 RCV003610816 RCV003609985 RCV003811006 RCV003843896 RCV003849029 RCV003871499 RCV004595000 RCV001050515 RCV001222824 RCV001207191	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Familial cancer of breast	Pathogenic	rs777414552	RCV005869997	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability	Likely pathogenic	rs1907323150	RCV001291094	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MLYCD-related disorder	Likely pathogenic; Pathogenic	rs1179555424	RCV003400485	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Sarcoma	Pathogenic	rs761146008	RCV005887290	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CARDIOMYOPATHIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
KERATOCONUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALONIC ACIDEMIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALONIC ACIDURIA	—	CTD, ClinGen, Disgenet, GenCC, Orphanet CTD, ClinGen, Disgenet, GenCC, Orphanet CTD, ClinGen, Disgenet, GenCC, Orphanet CTD, ClinGen, Disgenet, GenCC, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALONYL-COA DECARBOXYLASE DEFICIENCY	—	HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROBLASTOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRIMARY CARDIOMYOPATHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acute Kidney Tubular Necrosis	Renal tubular necrosis	BEFREE	29131245		★☆☆☆☆ Found in Text Mining only
Angiolymphoid hyperplasia	Angiolymphoid Hyperplasia	BEFREE	29143319, 29157611, 31242229, 31296233		★☆☆☆☆ Found in Text Mining only
ANOPHTHALMIA AND PULMONARY HYPOPLASIA	Syndromic microphthalmia	BEFREE	29050294		★☆☆☆☆ Found in Text Mining only
Aortic Valve Disease	Aortic valve disease	Pubtator	27250500	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	37729394	Inhibit	★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	BEFREE	12955715, 16275149		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Corneal Dystrophy, Juvenile Epithelial of Meesmann	Corneal Dystrophy, Epithelial Of Meesmann	BEFREE	18806880		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	21816445		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	BEFREE	15578582		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Fatty Liver	Fatty Liver	BEFREE	28325574, 30202895, 30249323		★☆☆☆☆ Found in Text Mining only
Fatty Liver Disease	Fatty Liver	BEFREE	24597775, 28346483, 28632778, 29278707, 30249323, 30579258		★☆☆☆☆ Found in Text Mining only
Fibrosis, Liver	Liver Fibrosis	BEFREE	29278707		★☆☆☆☆ Found in Text Mining only
Focal glomerulosclerosis	Glomerulosclerosis	BEFREE	16013025		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	20549361		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydrocephalus, Normal Pressure	Hydrocephalus	BEFREE	9719147		★☆☆☆☆ Found in Text Mining only
Hypertensive disease	Hypertension	BEFREE	20702857		★☆☆☆☆ Found in Text Mining only
Hypertrophic Cardiomyopathy	Hypertrophic cardiomyopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Immunologic Deficiency Syndromes	Immunologic Deficiency Syndromes	BEFREE	19470786, 29143319		★☆☆☆☆ Found in Text Mining only
Inborn Errors of Metabolism	Inborn Errors Of Metabolism	BEFREE	16275149, 20549361		★☆☆☆☆ Found in Text Mining only
Kaposi Sarcoma	Kaposi Sarcoma	BEFREE	17698410, 29143319, 29157611, 29766014, 31242229		★☆☆☆☆ Found in Text Mining only
Ketosis	Ketosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney Disease	BEFREE	9536096, 9719147		★☆☆☆☆ Found in Text Mining only
Lipoid nephrosis	Lipoid Nephrosis	BEFREE	14569107, 16013025		★☆☆☆☆ Found in Text Mining only
Lymphoma	Lymphoma	BEFREE	28143881		★☆☆☆☆ Found in Text Mining only
Lymphoproliferative Disorders	Lymphoproliferative Disorder	BEFREE	31296233		★☆☆☆☆ Found in Text Mining only
Macular dystrophy, corneal type 1	Macular corneal dystrophy	BEFREE	31242229		★☆☆☆☆ Found in Text Mining only
Malformations of Cortical Development	Malformation of cortical development	BEFREE	16275149, 27750396		★☆☆☆☆ Found in Text Mining only
Malonic aciduria	Malonic aciduria	Pubtator	32602666, 34884438, 8259873	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malonic aciduria	Malonic aciduria	Pubtator	34884438	Inhibit	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Membranous glomerulonephritis	Membranous Glomerulonephritis	BEFREE	16013025		★☆☆☆☆ Found in Text Mining only
Metaphyseal chondrodysplasia Schmid type	Metaphyseal chondrodysplasia	BEFREE	25542771		★☆☆☆☆ Found in Text Mining only
Mild Mental Retardation	Mental retardation	BEFREE	9869665		★☆☆☆☆ Found in Text Mining only
Multiple renal cysts	Multiple renal cysts	BEFREE	9719147		★☆☆☆☆ Found in Text Mining only
Nasopharyngeal carcinoma	Nasopharyngeal Carcinoma	GWASDB_DG	23209447		★☆☆☆☆ Found in Text Mining only
Neonatal hypoglycemia	Hypoglycemia	BEFREE	24613099		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	19470786, 29050294		★☆☆☆☆ Found in Text Mining only
Nephronophthisis	Nephronophthisis	BEFREE	9719147		★☆☆☆☆ Found in Text Mining only
Nephronophthisis 1	Nephronophthisis	BEFREE	9719147		★☆☆☆☆ Found in Text Mining only
Nephronophthisis, familial juvenile	Nephronophthisis	BEFREE	9719147		★☆☆☆☆ Found in Text Mining only
Nephrosclerosis	Nephrosclerosis	BEFREE	14569107		★☆☆☆☆ Found in Text Mining only
Nephrotic Syndrome	Nephrotic Syndrome	BEFREE	29131245		★☆☆☆☆ Found in Text Mining only
Non-alcoholic Fatty Liver Disease	Non-Alcoholic Fatty Liver Disease	BEFREE	29975946, 30236852		★☆☆☆☆ Found in Text Mining only
Nonalcoholic Steatohepatitis	Non-alcoholic Fatty Liver Disease	BEFREE	29278707		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	16721829		★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	Pubtator	37976137	Associate	★☆☆☆☆ Found in Text Mining only
Renal glomerular disease	Renal Glomerular Disease	BEFREE	12397035		★☆☆☆☆ Found in Text Mining only
Retinoblastoma	Retinoblastoma	Pubtator	37603355	Associate	★☆☆☆☆ Found in Text Mining only
Steatohepatitis	Fatty Liver	BEFREE	28325574, 28346483, 28895119, 29278707, 30202895, 30249323		★☆☆☆☆ Found in Text Mining only
Tuberous Sclerosis	Tuberous Sclerosis	BEFREE	27750396		★☆☆☆☆ Found in Text Mining only