MBD3L2

methyl-CpG binding domain protein 3 like 2

Basic information

Region (hg38): 19:7049321-7051735

Links

ENSG00000230522

∙ NCBI:125997 ∙ OMIM:607964 ∙ HGNC:18532 ∙ Uniprot:Q8NHZ7 ∙ 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 MBD3L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MBD3L2 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 clinvar		1
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	1	0

Variants in MBD3L2

This is a list of pathogenic ClinVar variants found in the MBD3L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-7051382-A-G			Likely benign (Nov 01, 2024)	2649148

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MBD3L2	protein_coding	protein_coding	ENST00000381393	2	2415

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.361	54	47.0	1.15	0.00000288	1262
Missense in Polyphen		7	10.332	0.67749		331
Synonymous	0.0252	19	19.1	0.993	0.00000108	433
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

Pathway: Signaling events mediated by HDAC Class I (Consensus)

Recessive Scores

pRec: 0.0677

Haploinsufficiency Scores

pHI
hipred
hipred_score
ghis: 0.419

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.361

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mbd3l2
Phenotype: normal phenotype;

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;methylation-dependent chromatin silencing
Cellular component: nucleus
Molecular function: methyl-CpG binding