BAHD1
protein-codingbromo adjacent homology domain containing 1
Gene summary
Enables chromatin binding activity. Involved in heterochromatin formation and negative regulation of DNA-templated transcription. Located in nucleoplasm. Part of chromatin silencing complex. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.5 kbGenCC 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 BAHD1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014952.5. 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 | 1 | ||||
| missense | 131 | 1 | 132 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 132 | 2 | 0 | 134 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055767.3 | 6 | MANE Select | |
| Ensembl | ENSP00000396976.1 | 6 | MANE Select | |
| RefSeq | NP_001288061.1 | 6 | Standard | |
| RefSeq | NP_001397973.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- heterochromatin assembly
- negative regulation of transcription, DNA-templated
Molecular Function
- chromatin binding
- protein binding
Cellular Component
- nucleoplasm
- chromatin silencing complex
- chromosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000416165
- Coding exons
- 6
- Length
- 28522
- Individuals with no LoFs
- 125624
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 118
- Defined
- 125742
- p
- 0.000469
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.31 | 435 | 519 | 0.838 | 0.0000344 | 4947 |
| Missense (PolyPhen) | 172 | 251.48 | 0.68396 | 2257 | ||
| Synonymous | 0.142 | 200 | 203 | 0.987 | 0.0000124 | 1755 |
| Loss of Function | 4.44 | 4 | 30.5 | 0.131 | 0.00000204 | 292 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0014 | 0.0014 | notable |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00082 | 0.00082 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00014 | 0.00014 | rare |
| South Asian | 0.0019 | 0.0019 | notable |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Heterochromatin protein that acts as a transcription repressor and has the ability to promote the formation of large heterochromatic domains. May act by recruiting heterochromatin proteins such as CBX5 (HP1 alpha), HDAC5 and MBD1. Represses IGF2 expression by binding to its CpG-rich P3 promoter and recruiting heterochromatin proteins. At specific stages of Listeria infection, in complex with TRIM28, corepresses interferon- stimulated genes, including IFNL1, IFNL2 and IFNL3. {ECO:0000269|PubMed:19666599, ECO:0000269|PubMed:21252314}.;
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- LoFtool
- 0.260
- RVIS EVS
- -0.93
- RVIS percentile EVS
- 9.72
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- K
- Indispensability pred.
- E
- Indispensability score
- 0.824
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |