MBD1 (methyl-CpG binding domain protein 1)

Gene

• Entrez ID: 4152
• Gene name: Methyl-CpG binding domain protein 1
• Gene symbol: MBD1
• Synonyms (NCBI Gene): CXXC3, PCM1, RFT
• Chromosome: 18
• Chromosome location: 18q21.1
• Summary: The protein encoded by this gene is a member of a family of nuclear proteins related by the presence of a methyl-CpG binding domain (MBD). These proteins are capable of binding specifically to methylated DNA, and some members can also repress transcriptio

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT007219	hsa-miR-195-5p	Luciferase reporter assay	23349673
MIRT050283	hsa-miR-25-3p	CLASH	23622248
MIRT047606	hsa-miR-10a-5p	CLASH	23622248
MIRT040325	hsa-miR-615-3p	CLASH	23622248
MIRT690077	hsa-miR-18a-5p	HITS-CLIP	23313552
MIRT690076	hsa-miR-18b-5p	HITS-CLIP	23313552
MIRT690075	hsa-miR-4735-3p	HITS-CLIP	23313552
MIRT690074	hsa-miR-6504-3p	HITS-CLIP	23313552
MIRT690073	hsa-miR-4761-5p	HITS-CLIP	23313552
MIRT690072	hsa-miR-6814-5p	HITS-CLIP	23313552
MIRT690071	hsa-miR-1234-3p	HITS-CLIP	23313552
MIRT690070	hsa-miR-7107-5p	HITS-CLIP	23313552
MIRT690069	hsa-miR-150-5p	HITS-CLIP	23313552
MIRT690068	hsa-miR-1913	HITS-CLIP	23313552
MIRT690067	hsa-miR-324-3p	HITS-CLIP	23313552
MIRT690066	hsa-miR-18a-3p	HITS-CLIP	23313552
MIRT690065	hsa-miR-619-5p	HITS-CLIP	23313552
MIRT690064	hsa-miR-6506-5p	HITS-CLIP	23313552
MIRT690063	hsa-miR-4707-3p	HITS-CLIP	23313552
MIRT690062	hsa-miR-6778-3p	HITS-CLIP	23313552
MIRT690061	hsa-miR-4731-5p	HITS-CLIP	23313552
MIRT690060	hsa-miR-5589-5p	HITS-CLIP	23313552
MIRT690059	hsa-miR-5095	HITS-CLIP	23313552
MIRT690058	hsa-miR-7151-3p	HITS-CLIP	23313552
MIRT690057	hsa-miR-5089-5p	HITS-CLIP	23313552
MIRT678996	hsa-miR-4797-5p	HITS-CLIP	23824327
MIRT678994	hsa-miR-5007-5p	HITS-CLIP	23824327
MIRT678995	hsa-miR-4524a-3p	HITS-CLIP	23824327
MIRT678992	hsa-miR-3672	HITS-CLIP	23824327
MIRT678993	hsa-miR-6864-3p	HITS-CLIP	23824327
MIRT678991	hsa-miR-8055	HITS-CLIP	23824327
MIRT290618	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT690077	hsa-miR-18a-5p	HITS-CLIP	23313552
MIRT690076	hsa-miR-18b-5p	HITS-CLIP	23313552
MIRT690075	hsa-miR-4735-3p	HITS-CLIP	23313552
MIRT690074	hsa-miR-6504-3p	HITS-CLIP	23313552
MIRT690073	hsa-miR-4761-5p	HITS-CLIP	23313552
MIRT690072	hsa-miR-6814-5p	HITS-CLIP	23313552
MIRT690071	hsa-miR-1234-3p	HITS-CLIP	23313552
MIRT690070	hsa-miR-7107-5p	HITS-CLIP	23313552
MIRT690069	hsa-miR-150-5p	HITS-CLIP	23313552
MIRT690068	hsa-miR-1913	HITS-CLIP	23313552
MIRT690067	hsa-miR-324-3p	HITS-CLIP	23313552
MIRT690066	hsa-miR-18a-3p	HITS-CLIP	23313552
MIRT690065	hsa-miR-619-5p	HITS-CLIP	23313552
MIRT690064	hsa-miR-6506-5p	HITS-CLIP	23313552
MIRT690063	hsa-miR-4707-3p	HITS-CLIP	23313552
MIRT690062	hsa-miR-6778-3p	HITS-CLIP	23313552
MIRT690061	hsa-miR-4731-5p	HITS-CLIP	23313552
MIRT690060	hsa-miR-5589-5p	HITS-CLIP	23313552
MIRT690059	hsa-miR-5095	HITS-CLIP	23313552
MIRT690058	hsa-miR-7151-3p	HITS-CLIP	23313552
MIRT690057	hsa-miR-5089-5p	HITS-CLIP	23313552
MIRT678996	hsa-miR-4797-5p	HITS-CLIP	23824327
MIRT678994	hsa-miR-5007-5p	HITS-CLIP	23824327
MIRT678995	hsa-miR-4524a-3p	HITS-CLIP	23824327
MIRT678992	hsa-miR-3672	HITS-CLIP	23824327
MIRT678993	hsa-miR-6864-3p	HITS-CLIP	23824327
MIRT678991	hsa-miR-8055	HITS-CLIP	23824327
MIRT290618	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT1134787	hsa-miR-1343	CLIP-seq
MIRT1134788	hsa-miR-4268	CLIP-seq
MIRT1134789	hsa-miR-4286	CLIP-seq
MIRT1134790	hsa-miR-4448	CLIP-seq
MIRT1134791	hsa-miR-498	CLIP-seq
MIRT1134792	hsa-miR-4676-5p	CLIP-seq
MIRT1134793	hsa-miR-575	CLIP-seq
MIRT1134794	hsa-miR-634	CLIP-seq
MIRT1134795	hsa-miR-125a-3p	CLIP-seq
MIRT1134796	hsa-miR-3157-5p	CLIP-seq
MIRT1134797	hsa-miR-33a	CLIP-seq
MIRT1134798	hsa-miR-33b	CLIP-seq
MIRT1134799	hsa-miR-3934	CLIP-seq
MIRT1134800	hsa-miR-4291	CLIP-seq
MIRT1134801	hsa-miR-4310	CLIP-seq
MIRT1134802	hsa-miR-4424	CLIP-seq
MIRT1134803	hsa-miR-4461	CLIP-seq
MIRT1134804	hsa-miR-4468	CLIP-seq
MIRT1134805	hsa-miR-4519	CLIP-seq
MIRT1134806	hsa-miR-4691-3p	CLIP-seq
MIRT1134807	hsa-miR-4792	CLIP-seq
MIRT1134808	hsa-miR-764	CLIP-seq
MIRT2442351	hsa-miR-3124-3p	CLIP-seq
MIRT2442352	hsa-miR-4274	CLIP-seq
MIRT1134805	hsa-miR-4519	CLIP-seq
MIRT2465608	hsa-miR-1915	CLIP-seq
MIRT2465609	hsa-miR-624	CLIP-seq
MIRT2465610	hsa-miR-720	CLIP-seq
MIRT2567884	hsa-miR-1287	CLIP-seq
MIRT2567885	hsa-miR-1293	CLIP-seq
MIRT2567886	hsa-miR-216b	CLIP-seq
MIRT2567887	hsa-miR-3135b	CLIP-seq
MIRT1134796	hsa-miR-3157-5p	CLIP-seq
MIRT1134797	hsa-miR-33a	CLIP-seq
MIRT1134798	hsa-miR-33b	CLIP-seq
MIRT2567888	hsa-miR-376a	CLIP-seq
MIRT2567889	hsa-miR-376b	CLIP-seq
MIRT2567890	hsa-miR-4314	CLIP-seq
MIRT2567891	hsa-miR-4417	CLIP-seq
MIRT2567892	hsa-miR-4483	CLIP-seq
MIRT1134792	hsa-miR-4676-5p	CLIP-seq
MIRT2567893	hsa-miR-541	CLIP-seq
MIRT1134793	hsa-miR-575	CLIP-seq
MIRT1134794	hsa-miR-634	CLIP-seq
MIRT2567894	hsa-miR-642b	CLIP-seq
MIRT2567895	hsa-miR-654-5p	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
HDAC3	Unknown	16432238

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IBA
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	TAS	9774669
GO:0005515	Function	Protein binding	IPI	12665582, 12711603, 16432238, 19498464, 19666599, 21653829, 23275563
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	10454587
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0006346	Process	DNA methylation-dependent constitutive heterochromatin formation	IBA
GO:0006366	Process	Transcription by RNA polymerase II	TAS	9774669
GO:0008270	Function	Zinc ion binding	IDA	29276034
GO:0008270	Function	Zinc ion binding	IEA
GO:0008327	Function	Methyl-CpG binding	IBA
GO:0008327	Function	Methyl-CpG binding	IDA	25284789
GO:0008327	Function	Methyl-CpG binding	NAS	10454587
GO:0010385	Function	Double-stranded methylated DNA binding	IDA	11371345
GO:0016363	Component	Nuclear matrix	IEA
GO:0016363	Component	Nuclear matrix	ISS
GO:0016607	Component	Nuclear speck	IEA
GO:0016607	Component	Nuclear speck	ISS
GO:0045322	Function	Unmethylated CpG binding	IDA	29276034
GO:0045892	Process	Negative regulation of DNA-templated transcription	NAS	10454587
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 156535
• HGNC: 6916
• e!Ensembl: ENSG00000141644

Protein

• UniProt ID: Q9UIS9
• Protein name: Methyl-CpG-binding domain protein 1 (CXXC-type zinc finger protein 3) (Methyl-CpG-binding protein MBD1) (Protein containing methyl-CpG-binding domain 1)
• Protein function: Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (
• PDB: 1D9N, 1IG4, 4D4W, 5W9Q, 6D1T
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01429	MBD	1 → 88	Methyl-CpG binding domain	Domain
  PF02008	zf-CXXC	168 → 215	CXXC zinc finger domain	Domain
  PF02008	zf-CXXC	217 → 262	CXXC zinc finger domain	Domain
  PF02008	zf-CXXC	330 → 377	CXXC zinc finger domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:9207790}.
• Sequence:

  MAEDWLDCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPACDLT
  LFDFKQGILCYPAPKAHPVAVASKKRKKPSRPAKTRKRQVGPQSGEVRKEAPRDETKADT
  DTAPASFPAPGCCENCGISFSGDGTQRQRLKTLCKDCRAQRIAFNREQRMFKRVGCGECA
  ACQVTEDCGACSTCLLQLPHDVASGLFCKCERRRCLRIVERSRGCGVCRGCQTQEDCGHC
  PICLRPPRPGLRRQWKCVQRRCLRGKHARRKGGCDSKMAARRRPGAQPLPPPPPSQSPEP
  TEPHPRALAPSPPAEFIYYCVDEDELQPYTNRRQNRKCGACAACLRRMDCGRCDFCCDKP
  KFGGSNQKRQKCRWRQCLQFAMKRLLPSVWSESEDGAGSPPPYRRRKRPSSARRHHLGPT
  LKPTLATRTAQPDHTQAPTKQEAGGGFVLPPPGTDLVFLREGASSPVQVPGPVAASTEAL
  LQEAQCSGLSWVVALPQVKQEKADTQDEWTPGTAVLTSPVLVPGCPSKAVDPGLPSVKQE
  PPDPEEDKEENKDDSASKLAPEEEAGGAGTPVITEIFSLGGTRFRDTAVWLPRSKDLKKP
  GARKQ

• Sequence length: 605

Pathways

Reactome:

SUMOylation of transcription cofactors

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
MBD1-related disorder	Uncertain significance; Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATIC NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma	Adenocarcinoma	BEFREE	16284366		★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	LHGDN	12384770, 12770674		★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	BEFREE	15967618, 18385101, 20499253		★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	Pubtator	19921286	Associate	★☆☆☆☆ Found in Text Mining only
Biliary Atresia	Biliary Atresia	BEFREE	21857377		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	21105050		★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	18445260	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	18445260		★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	16284366, 18668384		★☆☆☆☆ Found in Text Mining only
Colonic Neoplasms	Colonic neoplasm	Pubtator	19074829	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	28473981	Inhibit	★☆☆☆☆ Found in Text Mining only
Complete atrioventricular block	Complete Atrioventricular Block	BEFREE	28065745		★☆☆☆☆ Found in Text Mining only
Congenital atresia of extrahepatic bile duct	Extrahepatic Biliary Atresia	BEFREE	21857377		★☆☆☆☆ Found in Text Mining only
Gallbladder Carcinoma	Gallbladder cancer	BEFREE	31516389		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	10187827	Associate	★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	15081425		★☆☆☆☆ Found in Text Mining only
Heart Diseases	Heart disease	Pubtator	27744583	Associate	★☆☆☆☆ Found in Text Mining only
Hepatolenticular Degeneration	Hepatolenticular Degeneration	BEFREE	27744583, 31321400		★☆☆☆☆ Found in Text Mining only
Hepatolenticular Degeneration	Hepatolenticular degeneration	Pubtator	27744583	Associate	★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	30385847	Associate	★☆☆☆☆ Found in Text Mining only
leiomyosarcoma	Leiomyosarcoma	BEFREE	30900935		★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung Neoplasms	LHGDN	18668384		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	21105050		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of gallbladder	Gallbladder cancer	BEFREE	31516389		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	12776203, 16284366, 18668384		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	18445260, 19276660, 23331011, 23588667, 26980696, 30487699		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	12646234, 18666890		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	CTD_human_DG	29610475		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	12646234		★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	BEFREE	26339430		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	18445260, 19276660, 23331011		★☆☆☆☆ Found in Text Mining only
Osteoarthritis	Osteoarthritis	Pubtator	30385847	Inhibit	★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	Pubtator	30385847	Inhibit	★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	14599962, 18445260, 19276660, 23331011, 23588667, 26980696, 30487699		★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasm	Pancreatic Neoplasm	LHGDN	18445260		★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	18445260, 19276660, 30487699	Associate	★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	12646234, 18666890		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic Neoplasms	CTD_human_DG	29610475		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Rett Syndrome	Rett Syndrome	LHGDN	12770674		★☆☆☆☆ Found in Text Mining only
Rett Syndrome	Rett Syndrome	BEFREE	19813260		★☆☆☆☆ Found in Text Mining only
Scleroderma	Scleroderma	BEFREE	9540072		★☆☆☆☆ Found in Text Mining only
Systemic Scleroderma	Scleroderma	BEFREE	9540072		★☆☆☆☆ Found in Text Mining only
Thyroid Neoplasm	Thyroid Neoplasm	BEFREE	10980597, 15368067		★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Uterine neoplasm	Pubtator	32469064	Associate	★☆☆☆☆ Found in Text Mining only
Vitiligo	Vitiligo	BEFREE	20560952		★☆☆☆☆ Found in Text Mining only
VITILIGO-ASSOCIATED MULTIPLE AUTOIMMUNE DISEASE SUSCEPTIBILITY 1 (finding)	Vitiligo-associated SYSTEMIC LUPUS ERYTHEMATOSUS	BEFREE	20560952		★☆☆☆☆ Found in Text Mining only