MBD1

methyl-CpG binding domain protein 1, the group of Zinc fingers CXXC-type|Methyl-CpG binding domain containing

Basic information

Region (hg38): 18:50266881-50281774

Links

ENSG00000141644 ∙ NCBI:4152 ∙ OMIM:156535 ∙ HGNC:6916 ∙ Uniprot:Q9UIS9 ∙ 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 MBD1 gene.

• Inborn genetic diseases (18 variants)
• not provided (4 variants)
• not specified (2 variants)
• MBD1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MBD1 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				3	1	4
missense			18			18
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	1

Variants in MBD1

This is a list of pathogenic ClinVar variants found in the MBD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-50267603-G-A		MBD1-related disorder	Benign (Mar 20, 2019)
18-50269647-G-A		MBD1-related disorder	Benign (Jul 12, 2019)
18-50269822-C-G		MBD1-related disorder	Likely benign (Jul 10, 2019)
18-50270029-A-C		MBD1-related disorder	Benign (Feb 01, 2024)
18-50272708-G-A		not specified	Uncertain significance (Feb 16, 2023)
18-50272885-T-C		not specified	Uncertain significance (Apr 29, 2022)
18-50273360-C-T		not specified	Uncertain significance (May 09, 2023)
18-50273404-G-A		not specified	Uncertain significance (Dec 14, 2022)
18-50273600-C-T		not specified • MBD1-related disorder	Likely benign (Apr 11, 2019)
18-50273623-C-T		not specified	Uncertain significance (Feb 28, 2024)
18-50273657-C-T		MBD1-related disorder	Likely benign (Mar 01, 2023)
18-50273668-C-T		not specified	Uncertain significance (Feb 22, 2023)
18-50273706-G-A		not specified	Conflicting classifications of pathogenicity (Jul 09, 2021)
18-50273773-G-A			Uncertain significance (Mar 09, 2023)
18-50273799-C-T		not specified	Likely benign (Sep 22, 2023)
18-50273809-G-C		MBD1-related disorder	Benign (Oct 21, 2019)
18-50273810-G-A			Likely benign (Jul 01, 2022)
18-50273845-C-T		not specified	Uncertain significance (Oct 20, 2021)
18-50273849-G-C		MBD1-related disorder	Likely benign (Apr 03, 2019)
18-50274295-C-T		not specified	Uncertain significance (Aug 12, 2022)
18-50275006-T-C		not specified	Uncertain significance (Feb 23, 2023)
18-50275011-T-G		MBD1-related disorder	Uncertain significance (Dec 06, 2022)
18-50275137-T-C		not specified	Uncertain significance (Nov 12, 2021)
18-50275177-C-T		MBD1-related disorder	Likely benign (Jun 12, 2019)
18-50275376-G-A		MBD1-related disorder	Likely benign (Aug 21, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MBD1	protein_coding	protein_coding	ENST00000590208	15	14893

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00283	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	290	403	0.721	0.0000281	4184
Missense in Polyphen		68	167.1	0.40695		1705
Synonymous	-0.509	160	152	1.05	0.00000962	1351
Loss of Function	5.07	5	39.3	0.127	0.00000252	411

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000446	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters. {ECO:0000269|PubMed:10454587, ECO:0000269|PubMed:10648624, ECO:0000269|PubMed:12665582, ECO:0000269|PubMed:12697822, ECO:0000269|PubMed:12711603, ECO:0000269|PubMed:14555760, ECO:0000269|PubMed:14610093, ECO:0000269|PubMed:15327775, ECO:0000269|PubMed:9207790, ECO:0000269|PubMed:9774669}.
• Pathway: Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.0163
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.58

Haploinsufficiency Scores

• pHI: 0.764
• hipred: Y
• hipred_score: 0.583
• ghis: 0.675

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.885

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mbd1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cellular phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;methylation-dependent chromatin silencing;transcription by RNA polymerase II;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;chromosome;nuclear matrix;nuclear speck
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;zinc ion binding;methyl-CpG binding;double-stranded methylated DNA binding