MBTD1

protein-coding

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

Gene summary

Enables NuA4 histone acetyltransferase complex binding activity; histone H4K20me1 reader activity; and histone H4K20me2 reader activity. Involved in double-strand break repair via homologous recombination; positive regulation of double-strand break repair via homologous recombination; and regulation of cell cycle. Located in nucleoplasm. Part of NuA4 histone acetyltransferase complex. Is active in site of double-strand break. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_017643.3

Inheritance

—

ClinVar variants

U:47

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr17:51,177,425-51,260,163

External References & Databases

Ensembl (ENSG00000011258)

Transcript & Mutation Effects

hg38 • Region Span ~82.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MBTD1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 43

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017643.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			45 clinvar			45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	47	0	0	47

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017643.3	RefSeq	NP_060113.2	15	MANE Select
ENST00000586178.6	Ensembl	ENSP00000468304.1	15	MANE Select
ENST00000376381.3	Ensembl	ENSP00000365561.3	9	Standard
ENST00000405860.7	Ensembl	ENSP00000386072.3	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Mesodermal Commitment Pathway

Biological Process

chromatin organization
regulation of transcription, DNA-templated
embryonic skeletal system development

Molecular Function

zinc ion binding
methylated histone binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000586178
Coding exons: 15
Length: 82739
Individuals with no LoFs: 125686
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125687
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.45	150	325	0.462	0.0000164	4136
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0830

Intolerance Scores

LoFtool: 0.119
RVIS EVS: 0.06
RVIS percentile EVS: 58.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.943

Gene Damage Prediction

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