Gene Gene information from NCBI Gene database.
Entrez ID 8930
Gene name Methyl-CpG binding domain 4, DNA glycosylase
Gene symbol MBD4
Synonyms (NCBI Gene)
MED1TPDS2UVM1
Chromosome 3
Chromosome location 3q21.3
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 miRNA information provided by mirtarbase database.
447
miRTarBase ID miRNA Experiments Reference
MIRT473395 hsa-miR-651-3p PAR-CLIP 20371350
MIRT473394 hsa-miR-4779 PAR-CLIP 20371350
MIRT473393 hsa-miR-1252-5p PAR-CLIP 20371350
MIRT473392 hsa-miR-6770-5p PAR-CLIP 20371350
MIRT473391 hsa-miR-1909-3p PAR-CLIP 20371350
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
20
GO ID Ontology Definition Evidence Reference
GO:0003677 Function DNA binding IBA
GO:0003677 Function DNA binding IEA
GO:0003696 Function Satellite DNA binding TAS 9774669
GO:0003824 Function Catalytic activity IEA
GO:0004520 Function DNA endonuclease activity TAS 10097147
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
603574 6919 ENSG00000129071
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O95243
Protein name Methyl-CpG-binding domain protein 4 (EC 3.2.2.-) (Methyl-CpG-binding endonuclease 1) (Methyl-CpG-binding protein MBD4) (Mismatch-specific DNA N-glycosylase)
Protein function Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyas
PDB 2MOE , 3IHO , 4DK9 , 4E9E , 4E9F , 4E9G , 4E9H , 4EA4 , 4EA5 , 4LG7 , 4OFA , 4OFE , 4OFH , 5CHZ , 6VJW , 7KZ0 , 7KZ1 , 7KZG
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF01429 MBD 76 151 Methyl-CpG binding domain Domain
Sequence
MGTTGLESLSLGDRGAAPTVTSSERLVPDPPNDLRKEDVAMELERVGEDEEQMMIKRSSE
CNPLLQEPIASAQFGATAGTECRKSVPCGWERVVKQRLFGKTAGRFDVYFISPQGLKFRS
KSSLANYLHKNGETSLKPEDFDFTVLSKRGI
KSRYKDCSMAALTSHLQNQSNNSNWNLRT
RSKCKKDVFMPPSSSSELQESRGLSNFTSTHLLLKEDEGVDDVNFRKVRKPKGKVTILKG
IPIKKTKKGCRKSCSGFVQSDSKRESVCNKADAESEPVAQKSQLDRTVCISDAGACGETL
SVTSEENSLVKKKERSLSSGSNFCSEQKTSGIINKFCSAKDSEHNEKYEDTFLESEEIGT
KVEVVERKEHLHTDILKRGSEMDNNCSPTRKDFTGEKIFQEDTIPRTQIERRKTSLYFSS
KYNKEALSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWK
FLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKY
GNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLS
Sequence length 580
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Base excision repair   Recognition and association of DNA glycosylase with site containing an affected pyrimidine
Cleavage of the damaged pyrimidine
Displacement of DNA glycosylase by APEX1
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
12
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 Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
MBD4-related disorder Likely pathogenic; Pathogenic rs778697654, rs769552413, rs769076971, rs558765093, rs897132425 RCV004757536
RCV004757594
RCV004757598
RCV003981042
RCV003896710
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Melanoma, uveal, susceptibility to, 1 Likely pathogenic; Pathogenic rs558765093, rs778697654, rs200758755 RCV005023267
RCV002274499
RCV002274502
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Ovarian serous cystadenocarcinoma Likely pathogenic; Pathogenic rs778697654 RCV005930210
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Tumor predisposition syndrome 2 Likely pathogenic; Pathogenic rs558765093, rs778697654, rs148098584, rs200758755, rs1559801181 RCV002274219
RCV002274500
RCV002274501
RCV002274503
RCV002274504
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
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.
Phenotype Name Clinical Significance Source Evidence Score
ANTI-TOPOISOMERASE-I-ANTIBODY-POSITIVE SYSTEMIC SCLERODERMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISTIC DISORDER CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Familial pancreatic carcinoma Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Hereditary cancer-predisposing syndrome Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute intermittent porphyria Intermittent Porphyria BEFREE 28412148
★☆☆☆☆
Found in Text Mining only
Acute monocytic leukemia Monocytic Leukemia BEFREE 30049810
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 16601283, 16803845
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma LHGDN 16803845
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 16601283
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of prostate Prostate adenocarcinoma BEFREE 23538858
★☆☆☆☆
Found in Text Mining only
Adenoma Adenoma BEFREE 16831587
★☆☆☆☆
Found in Text Mining only
Anaplastic thyroid carcinoma Anaplastic thyroid cancer BEFREE 15613457
★☆☆☆☆
Found in Text Mining only
Aortic Aneurysm Aortic Aneurysm BEFREE 31001930
★☆☆☆☆
Found in Text Mining only
Aortic Aneurysm Abdominal Aortic aneurysm Pubtator 31001930 Associate
★☆☆☆☆
Found in Text Mining only