MBTD1

mbt domain containing 1, the group of MBT domain containing|Tip60/Nua4 histone acetyltransferase complex subunits

Basic information

Region (hg38): 17:51177425-51260163

Links

ENSG00000011258 ∙ NCBI:54799 ∙ OMIM:618705 ∙ HGNC:19866 ∙ Uniprot:Q05BQ5 ∙ 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 MBTD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MBTD1 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	0

Variants in MBTD1

This is a list of pathogenic ClinVar variants found in the MBTD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-51180593-T-C		not specified	Uncertain significance (Feb 19, 2025)
17-51180641-G-C		not specified	Uncertain significance (Aug 19, 2024)
17-51180685-A-C		not specified	Uncertain significance (Jun 30, 2023)
17-51192905-T-C		not specified	Uncertain significance (Aug 04, 2024)
17-51192913-C-T		not specified	Uncertain significance (Jul 26, 2022)
17-51192953-G-A		not specified	Uncertain significance (Jul 19, 2023)
17-51192994-C-T		not specified	Uncertain significance (Oct 22, 2021)
17-51193505-T-C		not specified	Uncertain significance (Dec 27, 2023)
17-51201687-C-T		not specified	Uncertain significance (Jan 16, 2025)
17-51202724-A-G		not specified	Uncertain significance (Oct 30, 2024)
17-51202795-T-G		not specified	Uncertain significance (Feb 11, 2022)
17-51202874-C-T		not specified	Uncertain significance (Sep 29, 2022)
17-51202884-C-T		not specified	Uncertain significance (May 17, 2023)
17-51202923-T-C		not specified	Uncertain significance (Aug 09, 2021)
17-51203208-T-C		not specified	Uncertain significance (Jul 12, 2023)
17-51206905-C-T		not specified	Uncertain significance (Oct 26, 2024)
17-51206935-C-T		not specified	Uncertain significance (Oct 01, 2024)
17-51206990-A-T		not specified	Uncertain significance (Jun 16, 2024)
17-51207004-G-A		not specified	Uncertain significance (May 17, 2023)
17-51217371-T-C		not specified	Uncertain significance (Jul 26, 2024)
17-51217377-T-C		not specified	Uncertain significance (Jan 04, 2025)
17-51217378-T-G		not specified	Uncertain significance (Jan 24, 2025)
17-51218938-G-A		not specified	Uncertain significance (Jan 31, 2024)
17-51218959-G-A		not specified	Uncertain significance (Apr 20, 2024)
17-51225062-T-C		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MBTD1	protein_coding	protein_coding	ENST00000586178	15	82739

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	9.56e-7	125686	0	1	125687	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.45	150	325	0.462	0.0000164	4136
Missense in Polyphen		31	106.48	0.29114		1351
Synonymous	0.847	99	110	0.897	0.00000609	1140
Loss of Function	5.76	0	38.6	0.00	0.00000218	458

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative Polycomb group (PcG) protein. PcG proteins maintain the transcriptionally repressive state of genes, probably via a modification of chromatin, rendering it heritably changed in its expressibility (By similarity). Specifically binds to monomethylated and dimethylated 'Lys-20' on histone H4. {ECO:0000250, ECO:0000269|PubMed:19841675}.
• Disease: DISEASE: Note=A chromosomal aberration involving MBTD1 is a cause of acute poorly differentiated myeloid leukemia. Translocation (10;17)(p15;q21) with ZMYND11. {ECO:0000269|PubMed:23915195}.
• Pathway: Mesodermal Commitment Pathway (Consensus)

Recessive Scores

• pRec: 0.0830

Intolerance Scores

• loftool: 0.119
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.360
• hipred: Y
• hipred_score: 0.731
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.943

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mbtd1
• Phenotype: craniofacial phenotype; skeleton phenotype; liver/biliary system 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype

Gene ontology

• Biological process: chromatin organization;regulation of transcription, DNA-templated;embryonic skeletal system development
• Cellular component: nucleus
• Molecular function: zinc ion binding;methylated histone binding