Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	55777
Gene name Gene Name - the full gene name approved by the HGNC.	Methyl-CpG binding domain protein 5
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	MBD5
Synonyms (NCBI Gene) Gene synonyms aliases	C2DELq23.1, DEL2Q23.1, MRD1
Chromosome Chromosome number	2
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	2q23.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a member of the methyl-CpG-binding domain (MBD) family. The MBD consists of about 70 residues and is the minimal region required for a methyl-CpG-binding protein binding specifically to methylated DNA. In addition to the MBD domain, this

Show/Hide all(52)

SNP ID	Visualize variation	Clinical significance	Consequence
rs34995577	G>A	Likely-benign, likely-pathogenic, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, non coding transcript variant
rs115145637	A>G	Conflicting-interpretations-of-pathogenicity, likely-benign	Non coding transcript variant, synonymous variant, coding sequence variant
rs138058889	G>A,T	Conflicting-interpretations-of-pathogenicity, likely-benign	Non coding transcript variant, synonymous variant, coding sequence variant
rs141855494	A>C,G	Conflicting-interpretations-of-pathogenicity, benign-likely-benign	Non coding transcript variant, coding sequence variant, synonymous variant
rs145475623	C>T	Likely-benign, likely-pathogenic, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, non coding transcript variant
rs147455836	A>G	Likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, non coding transcript variant
rs151204004	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, synonymous variant, coding sequence variant
rs199530726	T>C	Likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, missense variant
rs200245855	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, missense variant
rs200287454	C>A,T	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained, missense variant
rs201668347	G>A,C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, missense variant
rs371014306	C>G	Conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, coding sequence variant
rs398122412	T>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs568826753	A>G	Likely-benign, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, missense variant
rs727503997	G>A	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, synonymous variant, coding sequence variant
rs771325235	G>A,T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, missense variant
rs773873513	A>G	Conflicting-interpretations-of-pathogenicity	Missense variant, non coding transcript variant, coding sequence variant
rs779662045	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, non coding transcript variant, synonymous variant
rs794727928	AAAAGCAT>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs796052719	TA>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs886041003	C>G	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs978179634	C>A,T	Likely-pathogenic	Synonymous variant, non coding transcript variant, coding sequence variant, stop gained
rs1057518567	A>-	Likely-pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1057524832	C>T	Likely-pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs1060501151	C>-,CC	Pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant
rs1060501153	AACT>-	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1064796473	G>A,T	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant, stop gained, non coding transcript variant
rs1085307859	C>T	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs1131691713	GGAT>-	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1553517456	G>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1553517973	CC>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1553517984	A>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1553517991	G>A	Pathogenic	Splice donor variant
rs1553518509	C>T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1553518511	->C	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1553518527	->AA	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1553518563	->C	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1553518593	C>T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1553518752	C>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1553519853	C>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1553520585	->T	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1553520624	C>A	Likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1553521650	A>T	Likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1559085550	T>G	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1559086213	C>T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1559087186	C>T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1559094754	ATCTGTTCTTCAAGATGGCGTCATAGTCACCACTGCAGCTGGAAACCCACTGCAGAGTCAGCTACCCATTGGGAGTGATTTT>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1559099927	C>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1574451881	A>T	Likely-pathogenic	Splice acceptor variant
rs1574459612	C>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1574461269	GA>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs1574484218	C>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant

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miRTarBase ID	miRNA	Experiments	Reference
MIRT016873	hsa-miR-335-5p	Microarray	18185580
MIRT498259	hsa-miR-6796-3p	PAR-CLIP	22291592
MIRT498258	hsa-miR-7151-5p	PAR-CLIP	22291592
MIRT498259	hsa-miR-6796-3p	PAR-CLIP	22291592
MIRT498258	hsa-miR-7151-5p	PAR-CLIP	22291592
MIRT2038404	hsa-miR-338-5p	CLIP-seq
MIRT2038405	hsa-miR-410	CLIP-seq
MIRT2038406	hsa-miR-4318	CLIP-seq
MIRT2038407	hsa-miR-4474-3p	CLIP-seq
MIRT2038408	hsa-miR-4799-5p	CLIP-seq
MIRT2268259	hsa-miR-4528	CLIP-seq
MIRT2268260	hsa-miR-664	CLIP-seq
MIRT2038405	hsa-miR-410	CLIP-seq
MIRT2038406	hsa-miR-4318	CLIP-seq
MIRT2038407	hsa-miR-4474-3p	CLIP-seq
MIRT2038408	hsa-miR-4799-5p	CLIP-seq

Show/Hide all(20)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003677	Function	DNA binding	IDA	20700456
GO:0003682	Function	Chromatin binding	IBA
GO:0003682	Function	Chromatin binding	IDA	20700456
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	20700456
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0007399	Process	Nervous system development	IMP	23587880
GO:0010369	Component	Chromocenter	IBA
GO:0010369	Component	Chromocenter	IDA	20700456
GO:0030496	Component	Midbody	IDA
GO:0040014	Process	Regulation of multicellular organism growth	ISS
GO:0042593	Process	Glucose homeostasis	ISS
GO:0050795	Process	Regulation of behavior	IMP	23587880
GO:0051239	Process	Regulation of multicellular organismal process	IEA
GO:0060399	Process	Positive regulation of growth hormone receptor signaling pathway	ISS
GO:0070062	Component	Extracellular exosome	HDA	19056867

MIM	HGNC	e!Ensembl
611472	20444	ENSG00000204406

Protein

UniProt ID

Q9P267

Protein name

Methyl-CpG-binding domain protein 5 (Methyl-CpG-binding protein MBD5)

Protein function

Non-catalytic component of the polycomb repressive deubiquitinase (PR-DUB) complex, a complex that specifically mediates deubiquitination of histone H2A monoubiquitinated at 'Lys-120' (H2AK119ub1) (PubMed:24634419). Important for stability of PR

Family and domains

Tissue specificity

TISSUE SPECIFICITY: Detected in heart, placenta, liver, skeletal muscle, kidney and pancreas. {ECO:0000269|PubMed:12529184}.

Sequence

MNGGKECDGGDKEGGLPAIQVPVGWQRRVDQNGVLYVSPSGSLLSCLEQVKTYLLTDGTC
KCGLECPLILPKVFNFDPGAAVKQRTAEDVKADEDVTKLCIHKRKIIAVATLHKSMEAPH
PSLVLTSPGGGTNATPVVPSRAATPRSVRNKSHEGITNSVMPECKNPFKLMIGSSNAMGR
LYVQELPGSQQQELHPVYPRQRLGSSEHGQKSPFRGSHGGLPSPASSGSQIYGDGSISPR
TDPLGSPDVFTRSNPGFHGAPNSSPIHLNRTPLSPPSVMLHGSPVQSSCAMAGRTNIPLS
PTLTTKSPVMKKPMCNFSTNMEIPRAMFHHKPPQGPPPPPPPSCALQKKPLTSEKDPLGI
LDPIPSKPVNQNPVIINPTSFHSNVHSQVPMMNVSMPPAVVPLPSNLPLPTVKPGHMNHG
SHVQRVQHSASTSLSPSPVTSPVHMMGTGIGRIEASPQRSRSSSTSSDHGNFMMPPVGPQ
ATSSGIKVPPRSPRSTIGSPRPSMPSSPSTKSDGHHQYKDIPNPLIAGISNVLNTPSSAA
FPTASAGSSSVKSQPGLLGMPLNQILNQHNAASFPASSLLSAAAKAQLANQNKLAGNNSS
SSSNSGAVAGSGNTEGHSTLNTMFPPTANMLLPTGEGQSGRAALRDKLMSQQKDALRKRK
QPPTTVLSLLRQSQMDSSAVPKPGPDLLRKQGQGSFPISSMSQLLQSMSCQSSHLSSNST
PGCGASNTALPCSANQLHFTDPSMNSSVLQNIPLRGEAVHCHNANTNFVHSNSPVPNHHL
AGLINQIQASGNCGMLSQSGMALGNSLHPNPPQSRISTSSTPVIPNSIVSSYNQTSSEAG
GSGPSSSIAIAGTNHPAITKTTSVLQDGVIVTTAAGNPLQSQLPIGSDFPFVGQEHALHF
PSNSTSNNHLPHPLNPSLLSSLPISLPVNQQHLLNQNLLNILQPSAGEGDMSSINNTLSN
HQLTHLQSLLNNNQMFPPNQQQQQLLQGYQNLQAFQGQSTIPCPANNNPMACLFQNFQVR
MQEDAALLNKRISTQPGLTALPENPNTTLPPFQDTPCELQPRIDPSLGQQVKDGLVVGGP
GDASVDAIYKAVVDAASKGMQVVITTAVNSTTQISPIPALSAMSAFTASIGDPLNLSSAV
SAVIHGRNMGGVDHDGRLRNSRGARLPKNLDHGKNVNEGDGFEYFKSASCHTSKKQWDGE
QSPRGERNRWKYEEFLDHPGHIHSSPCHERPNNVSTLPFLPGEQHPILLPPRNCPGDKIL
EENFRYNNYKRTMMSFKERLENTVERCAHINGNRPRQSRGFGELLSTAKQDLVLEEQSPS
SSNSLENSLVKDYIHYNGDFNAKSVNGCVPSPSDAKSISSEDDLRNPDSPSSNELIHYRP
RTFNVGDLVWGQIKGLTSWPGKLVREDDVHNSCQQSPEEGKVEPEKLKTLTEGLEAYSRV
RKRNRKSGKLNNHLEAAIHEAMSELDKMSGTVHQIPQGDRQMRPPKPKRRKISR

Sequence length

1494

Interactions

View interactions

	KEGG		Reactome
	Polycomb repressive complex		UCH proteinases

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Mental retardation	Intellectual disability, autosomal dominant 1, intellectual disability	rs398122412, rs1553518511, rs794727928, rs1553517984, rs796052719, rs1553518752, rs886041003, rs978179634, rs1057524832, rs1559099927, rs1060501153, rs1559094754, rs1060501151, rs1559087186, rs1553519853 View all (6 more)	N/A
autism spectrum disorder	Autism spectrum disorder	rs1553518509	N/A

Show/Hide Unknown Diseases (8)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Atrial Fibrillation	Atrial fibrillation	N/A	N/A	GWAS
Microcephaly	microcephaly	N/A	N/A	ClinVar
Myocardial Infarction	Myocardial infarction	N/A	N/A	GWAS
Neurodevelopmental Disorders	complex neurodevelopmental disorder	N/A	N/A	GenCC
Neuroticism	Neuroticism	N/A	N/A	GWAS
Non-Syndromic Intellectual Disability	autosomal dominant non-syndromic intellectual disability	N/A	N/A	GenCC
Schizophrenia	Schizophrenia	N/A	N/A	GWAS
seizure	Seizure	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (35)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Anxiety	Associate	23587880
Autism Spectrum Disorder	Associate	21981781, 23632792, 24885232, 25271084, 25853262, 34050248
Autism Spectrum Disorder	Inhibit	23055267
Autistic Disorder	Associate	21981781, 23055267, 23575222, 23632792, 31290275, 34050248, 37628781
Azoospermia Nonobstructive	Associate	38403804
Bipolar Disorder	Associate	23587880
Brain Diseases	Associate	24885232
Carcinoma Ovarian Epithelial	Associate	19603017
Child Behavior Disorders	Associate	23587880
Chromosome Aberrations	Associate	22521361
Chromosome Duplication	Stimulate	23632792
Corneal dystrophy epithelial basement membrane	Associate	22085900
Delayed Cranial Ossification due to CBFB Haploinsufficiency	Stimulate	19904302
Delayed Cranial Ossification due to CBFB Haploinsufficiency	Associate	36396431
Dementia	Associate	31290275
Depressive Disorder Treatment Resistant	Associate	31290275
Developmental Disabilities	Associate	23422940, 25853262, 26993267, 31290275, 34050248, 36396431, 37628781, 39300495
Epilepsy	Associate	21981781, 23055267, 28074849, 31290275, 37628781
Fetal Alcohol Spectrum Disorders	Associate	23587880
Fragile X Syndrome	Associate	25271084
Immotile cilia syndrome due to excessively long cilia	Associate	37628781
Intellectual Disability	Associate	17847001, 19904302, 21981781, 31290275, 36396431, 37628781
Mannose Binding Protein Deficiency	Associate	31290275
Mental Disorders	Associate	23055267, 34050248, 36396431
Mental Retardation Autosomal Dominant 1	Associate	25853262
Microcephaly	Associate	19904302
Mobility Limitation	Associate	23055267
Psychomotor Disorders	Associate	37628781
Rett Syndrome	Associate	19809484
Seizures	Associate	19904302, 36396431, 37628781
Sensation Disorders	Associate	29801487
Sleep Wake Disorders	Associate	25271084, 36396431
Smith Magenis Syndrome	Associate	25271084
Spasms Infantile	Associate	24885232
Speech Disorders	Associate	19904302, 23055267, 34050248, 36396431

MBD5 (methyl-CpG binding domain protein 5)