MBD2

methyl-CpG binding domain protein 2, the group of Methyl-CpG binding domain containing|Small nucleolar RNA protein coding host genes|NuRD complex subunits

Basic information

Region (hg38): 18:54151606-54224669

Links

ENSG00000134046 ∙ NCBI:8932 ∙ OMIM:603547 ∙ HGNC:6917 ∙ Uniprot:Q9UBB5 ∙ 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 MBD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MBD2 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					1	1
missense			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	1

Variants in MBD2

This is a list of pathogenic ClinVar variants found in the MBD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-54159821-T-C		not specified	Uncertain significance (Aug 05, 2023)
18-54159832-C-T		not specified	Uncertain significance (Mar 24, 2023)
18-54164588-A-G			Benign (Dec 31, 2019)
18-54188997-C-G		not specified	Uncertain significance (Dec 06, 2021)
18-54224091-G-C		not specified	Uncertain significance (Oct 26, 2021)
18-54224122-G-C		not specified	Uncertain significance (Nov 29, 2023)
18-54224150-C-A		not specified	Uncertain significance (Sep 22, 2022)
18-54224151-C-G		not specified	Uncertain significance (Sep 22, 2022)
18-54224185-C-A		not specified	Uncertain significance (Apr 19, 2023)
18-54224214-T-C		not specified	Uncertain significance (May 30, 2024)
18-54224223-C-A		not specified	Uncertain significance (Apr 07, 2023)
18-54224235-C-A		not specified	Uncertain significance (May 24, 2023)
18-54224237-C-T		not specified	Uncertain significance (May 15, 2024)
18-54224255-C-G		not specified	Uncertain significance (Feb 16, 2023)
18-54224271-G-A		not specified	Uncertain significance (Dec 11, 2023)
18-54224280-G-A		not specified	Uncertain significance (Dec 11, 2023)
18-54224352-C-T		not specified	Uncertain significance (Jun 05, 2023)
18-54224358-C-G		not specified	Uncertain significance (Apr 05, 2023)
18-54224367-T-C		not specified	Uncertain significance (Jun 06, 2023)
18-54224397-G-A		not specified	Uncertain significance (Oct 05, 2021)
18-54224400-C-G		not specified	Uncertain significance (Jul 11, 2022)
18-54224415-C-A		not specified	Uncertain significance (Dec 15, 2021)
18-54224429-G-A		not specified	Uncertain significance (Mar 28, 2023)
18-54224432-G-A		not specified	Uncertain significance (Dec 09, 2023)
18-54224432-G-T		not specified	Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MBD2	protein_coding	protein_coding	ENST00000256429	6	72080

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.350	0.650	125733	0	7	125740	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	85	160	0.531	0.00000775	2624
Missense in Polyphen		12	56.472	0.21249		751
Synonymous	1.06	48	58.2	0.824	0.00000303	850
Loss of Function	2.99	4	17.5	0.228	0.00000110	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000494	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binds hemimethylated DNA as well. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing. Functions as a scaffold protein, targeting GATAD2A and GATAD2B to chromatin to promote repression. May enhance the activation of some unmethylated cAMP-responsive promoters. {ECO:0000269|PubMed:10471499, ECO:0000269|PubMed:10947852, ECO:0000269|PubMed:12665568, ECO:0000269|PubMed:16415179, ECO:0000269|PubMed:24307175, ECO:0000269|PubMed:9774669}.
• Pathway: NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);RNA Polymerase I Promoter Clearance;RNA Polymerase I Promoter Opening;RNA Polymerase I Transcription;Signaling events mediated by HDAC Class I (Consensus)

Recessive Scores

• pRec: 0.328

Intolerance Scores

• loftool: 0.326
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.564
• hipred: Y
• hipred_score: 0.794
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.747

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mbd2
• 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); reproductive system phenotype; neoplasm; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin silencing at rDNA;methylation-dependent chromatin silencing;heart development;aging;response to mechanical stimulus;positive regulation of Wnt signaling pathway;response to nutrient levels;response to estradiol;cellular protein-containing complex assembly;positive regulation of chromatin binding;regulation of cell population proliferation;maternal behavior;ATP-dependent chromatin remodeling;regulation of DNA methylation;negative regulation of transcription, DNA-templated;embryonic organ development;cellular response to organic cyclic compound
• Cellular component: histone deacetylase complex;nuclear chromatin;heterochromatin;nucleus;nucleoplasm;cytosol;protein-containing complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;satellite DNA binding;mRNA binding;protein binding;methyl-CpG binding;protein domain specific binding;nucleosomal DNA binding;siRNA binding;C2H2 zinc finger domain binding