MBD3L1

methyl-CpG binding domain protein 3 like 1

Basic information

Region (hg38): 19:8832377-8843340

Previous symbols: [ "MBD3L" ]

Links

ENSG00000170948 ∙ NCBI:85509 ∙ OMIM:607963 ∙ HGNC:15774 ∙ Uniprot:Q8WWY6 ∙ 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 MBD3L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MBD3L1 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						0
missense			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in MBD3L1

This is a list of pathogenic ClinVar variants found in the MBD3L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-8842707-G-A		not specified	Uncertain significance (Mar 10, 2025)
19-8842739-G-C		not specified	Uncertain significance (Jul 05, 2023)
19-8842754-A-G		not specified	Uncertain significance (Mar 19, 2024)
19-8842785-A-C		not specified	Uncertain significance (Dec 17, 2021)
19-8842797-C-T		not specified	Uncertain significance (Jan 02, 2024)
19-8842841-T-A		not specified	Uncertain significance (Feb 08, 2025)
19-8842844-G-C		not specified	Uncertain significance (Oct 09, 2024)
19-8842865-C-G		not specified	Uncertain significance (May 15, 2023)
19-8842892-C-A		not specified	Uncertain significance (Feb 17, 2023)
19-8842929-C-T		not specified	Likely benign (Dec 03, 2021)
19-8842935-C-T		not specified	Uncertain significance (Oct 11, 2024)
19-8842995-T-C		not specified	Likely benign (Jan 19, 2024)
19-8843102-C-G		not specified	Uncertain significance (Feb 18, 2025)
19-8843160-T-C		not specified	Uncertain significance (Feb 27, 2024)
19-8843180-C-T		not specified	Uncertain significance (Jul 14, 2024)
19-8843193-T-G		not specified	Uncertain significance (Jan 22, 2025)
19-8843202-A-G		not specified	Uncertain significance (Jan 22, 2025)
19-8843249-C-A		not specified	Uncertain significance (Jan 03, 2022)
19-8843258-C-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MBD3L1	protein_coding	protein_coding	ENST00000595891	1	10943

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	0.106	99	102	0.970	0.00000498	1249
Missense in Polyphen		24	21.549	1.1138		302
Synonymous	0.652	34	39.2	0.868	0.00000202	382
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

• Function: FUNCTION: Transcriptional repressor. {ECO:0000269|PubMed:12504854}.

Recessive Scores

• pRec: 0.0957

Intolerance Scores

• loftool: 0.700
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.7

Haploinsufficiency Scores

• pHI: 0.0359
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.364

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mbd3l1
• Phenotype: normal phenotype

Gene ontology

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