MBD3

methyl-CpG binding domain protein 3, the group of NuRD complex subunits|Methyl-CpG binding domain containing

Basic information

Region (hg38): 19:1573596-1592865

Links

ENSG00000071655

∙ NCBI:53615 ∙ OMIM:603573 ∙ HGNC:6918 ∙ Uniprot:O95983 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MBD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MBD3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2 clinvar	1 clinvar	3
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	2	1

Variants in MBD3

This is a list of pathogenic ClinVar variants found in the MBD3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Significance	ClinVar
19-1581178-C-T	Likely benign (Aug 01, 2018)	719577
19-1584672-C-T	Benign (Dec 31, 2019)	712135
19-1592608-G-A	Likely benign (Oct 29, 2018)	793538

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MBD3	protein_coding	protein_coding	ENST00000156825	6	16244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.977	0.0235	125041	0	6	125047	0.0000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	145	200	0.724	0.0000148	1902
Missense in Polyphen		52	88.832	0.58538		743
Synonymous	-2.03	121	95.8	1.26	0.00000878	536
Loss of Function	3.14	0	11.5	0.00	4.96e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000998	0.0000998
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000326	0.0000266
Middle Eastern	0.00	0.00
South Asian	0.0000386	0.0000327
Other	0.000167	0.000164

dbNSFP

Source: dbNSFP

Function: FUNCTION: Acts as transcriptional repressor and plays a role in gene silencing. Does not bind to DNA by itself (PubMed:12124384). Binds to DNA with a preference for sites containing methylated CpG dinucleotides (in vitro). Binds to a lesser degree DNA containing unmethylated CpG dinucleotides (PubMed:24307175). Recruits histone deacetylases and DNA methyltransferases. {ECO:0000269|PubMed:10947852, ECO:0000269|PubMed:12124384, ECO:0000269|PubMed:18644863, ECO:0000269|PubMed:23361464, ECO:0000269|PubMed:24307175, ECO:0000269|PubMed:9774669}.;
Pathway: ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;Signal Transduction;Epigenetic regulation of gene expression;Gene expression (Transcription);downregulated of mta-3 in er-negative breast tumors;Generic Transcription Pathway;HDACs deacetylate histones;RNA Polymerase I Promoter Clearance;RNA Polymerase II Transcription;Chromatin modifying enzymes;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Chromatin organization;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Intracellular signaling by second messengers;Signaling events mediated by HDAC Class I (Consensus)

Recessive Scores

pRec: 0.129

Intolerance Scores

loftool: 0.0475
rvis_EVS: -0.82
rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

pHI: 0.207
hipred: Y
hipred_score: 0.771
ghis: 0.642

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.973

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Mbd3
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; digestive/alimentary phenotype; immune system phenotype; homeostasis/metabolism phenotype; cellular phenotype;

Zebrafish Information Network

Gene name: mbd3b
Affected structure: definitive hemopoiesis
Phenotype tag: abnormal
Phenotype quality: decreased occurrence

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;in utero embryonic development;methylation-dependent chromatin silencing;brain development;heart development;aging;tissue development;histone acetylation;histone deacetylation;response to nutrient levels;response to estradiol;ATP-dependent chromatin remodeling;regulation of DNA methylation;embryonic organ development
Cellular component: nuclear chromatin;heterochromatin;nucleus;nucleoplasm;cytoplasm;NuRD complex;protein-containing complex
Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA binding;histone deacetylase activity;protein binding;methyl-CpG binding;nucleosomal DNA binding