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	55777
Gene name	Methyl-CpG binding domain protein 5
Gene symbol	MBD5
Synonyms (NCBI Gene)	C2DELq23.1DEL2Q23.1MRD1
Chromosome	2
Chromosome location	2q23.1
Summary	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

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

1324

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autism spectrum disorder	Pathogenic; Likely pathogenic	rs2105571544, rs1553518509	RCV003127861 RCV000754667
Intellectual disability	Likely pathogenic; Pathogenic	rs1553518509, rs1680708290, rs1681481862	RCV001257688 RCV001257755 RCV001257754
Intellectual disability, autosomal dominant 1	Likely pathogenic; Pathogenic	rs2105627349, rs2105571544, rs2105622677, rs1293936199, rs766179352, rs2105633124, rs2105130509, rs2105124073, rs2105635449, rs1450731543, rs2105639771, rs2105124818, rs2105571301, rs2105131625, rs2105633619 View all (56 more)	RCV001376000 RCV001388646 RCV001381929 RCV001389526 RCV001387381 RCV001389351 RCV001385237 RCV001716993 RCV001974967 RCV001970189 RCV001989971 RCV001928699 RCV001927063 RCV002007142 RCV002002573 RCV001925710 RCV001964694 RCV001970036 RCV001956049 RCV001939035 RCV001962826 RCV002280276 RCV002280365 RCV002283952 RCV002289226 RCV002290138 RCV002291183 RCV002466345 RCV002468744 RCV000180349 RCV000258468 RCV002824389 RCV002852610 RCV003030672 RCV003018741 RCV003022353 RCV000258320 RCV003340906 RCV003389030 RCV003495012 RCV003494992 RCV003495647 RCV003495843 RCV003601783 RCV003602195 RCV003602533 RCV004555244 RCV001390694 RCV000459819 RCV000470180 RCV000547749 RCV000645266 RCV000645268 RCV000645272 RCV000645273 RCV005091889 RCV000680039 RCV000698489 RCV003495183 RCV000823426 RCV000815739 RCV001030998 RCV001004756 RCV001044074 RCV001197768 RCV001220215 RCV001223489 RCV000074465 RCV001241372 RCV001250386 RCV001255696
MBD5 associated neurodevelopmental disorder	Likely pathogenic; Pathogenic	rs1553518593	RCV003226341

Show/Hide Unknown Diseases (19)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Autistic behavior	Likely benign	rs2105278742	RCV001797852
Bilateral tonic-clonic seizure	Conflicting classifications of pathogenicity	rs148321416	RCV000678819
Chromosome 2q23.1 deletion syndrome	Conflicting classifications of pathogenicity	rs751251720	RCV000509498
Cleft palate	Conflicting classifications of pathogenicity	rs398124343	RCV005623291
Complex neurodevelopmental disorder	Uncertain significance	rs2105632032	RCV002226417
developmental delay with intractable seizures	Conflicting classifications of pathogenicity	rs149278000	RCV000678818
Gastric cancer	Conflicting classifications of pathogenicity	rs34995577	RCV005892082
Hypotonia	Uncertain significance	rs1226367404	RCV002246200
Intellectual disability, autosomal dominant	Uncertain significance	rs1201462027	RCV002272409
Intellectual Disability, Dominant	Conflicting classifications of pathogenicity; Uncertain significance	rs796052705, rs536900412, rs199626531, rs886054903, rs886054913, rs879943522, rs200561241	RCV000270835 RCV000364648 RCV000354473 RCV000322515 RCV000271278 RCV000326223 RCV000307619
Lung cancer	Likely benign	rs775650772	RCV005926050
Malignant tumor of esophagus	Benign	rs555177897	RCV005890933
Malignant tumor of urinary bladder	Uncertain significance	rs116235310	RCV005911172
MBD5-related disorder	Uncertain significance; Benign; Likely benign; Conflicting classifications of pathogenicity	rs763299719, rs114314967, rs1273991401, rs1682262158, rs77213206, rs143028540, rs2470027035, rs151204004, rs34995577, rs763275881, rs199530726, rs145808884, rs536900412, rs139964770, rs757922781 View all (25 more)	RCV003928841 RCV003891569 RCV003900448 RCV003913331 RCV003905207 RCV003937556 RCV003898894 RCV003927683 RCV003907633 RCV003955102 RCV003947541 RCV003967479 RCV003927742 RCV003907660 RCV003895225 RCV003947576 RCV003907659 RCV003937661 RCV003917715 RCV003955364 RCV003420567 RCV003405788 RCV003402559 RCV003416763 RCV003397691 RCV003414326 RCV003402110 RCV003400155 RCV003391467 RCV003896414 RCV003911651 RCV003957096 RCV003969495 RCV003959979 RCV003957910 RCV003912622 RCV003979995 RCV003979994 RCV003411703 RCV003393790
Melanoma	Likely benign	rs201821636	RCV005899978
Microcephaly	Conflicting classifications of pathogenicity	rs773716719	RCV001252862
See cases	Conflicting classifications of pathogenicity; Uncertain significance	rs878910680, rs1024254683, rs2105628183, rs796052712, rs781154198	RCV002252711 RCV002252748 RCV002252892 RCV002252034 RCV002252126
Seizure	Conflicting classifications of pathogenicity	rs564759063, rs775673512	RCV000781977 RCV000781978
Squamous cell carcinoma of the head and neck	Likely benign	rs775650772	RCV005926049

Show/Hide Text Mining Associations (35)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)