GeneBe

MBD1

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

Basic information

Region (hg38): 18:50266882-50281774

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.

  • not_specified (61 variants)
  • MBD1-related_disorder (9 variants)
  • not_provided (6 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. These statistics are base on transcript: NM_000015846.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
1
clinvar
 6
missense
56
clinvar
5
clinvar
 61
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 57 10 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MBD1protein_codingprotein_codingENST00000590208 1514893
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.9970.002831257370111257480.0000437
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.992904030.7210.00002814184
Missense in Polyphen68167.10.406951705
Synonymous-0.5091601521.050.000009621351
Loss of Function5.07539.30.1270.00000252411

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001230.000123
Ashkenazi Jewish0.00009930.0000992
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00004460.0000439
Middle Eastern0.00005440.0000544
South Asian0.0001310.0000653
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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