BAHD1

bromo adjacent homology domain containing 1

Basic information

Region (hg38): 15:40439721-40468236

Links

ENSG00000140320 ∙ NCBI:22893 ∙ OMIM:613880 ∙ HGNC:29153 ∙ Uniprot:Q8TBE0 ∙ 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 BAHD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BAHD1 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			81	1	1	83
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	81	1	1

Variants in BAHD1

This is a list of pathogenic ClinVar variants found in the BAHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-40458547-G-A		not specified	Uncertain significance (Oct 04, 2024)
15-40458564-G-A		not specified	Uncertain significance (Nov 10, 2022)
15-40458616-G-A		not specified	Uncertain significance (Apr 18, 2024)
15-40458619-G-A		not specified	Uncertain significance (Jul 12, 2023)
15-40458637-G-T		not specified	Uncertain significance (Dec 05, 2024)
15-40458714-C-T		not specified	Uncertain significance (Dec 22, 2024)
15-40458762-C-T		not specified	Uncertain significance (Jul 08, 2024)
15-40458788-C-A		not specified	Uncertain significance (Feb 07, 2023)
15-40458807-C-T		not specified	Uncertain significance (Aug 28, 2024)
15-40458832-A-G		not specified	Uncertain significance (Dec 13, 2022)
15-40458894-C-T		not specified	Uncertain significance (Jan 26, 2022)
15-40458895-G-A		not specified	Uncertain significance (Nov 15, 2024)
15-40458904-G-A		not specified	Uncertain significance (Aug 01, 2024)
15-40458921-C-T		not specified	Uncertain significance (Jul 09, 2021)
15-40458925-G-A		not specified	Uncertain significance (Feb 02, 2022)
15-40458928-G-A		not specified	Uncertain significance (Jun 06, 2023)
15-40458931-A-T		not specified	Uncertain significance (Nov 30, 2022)
15-40458933-C-G		not specified	Uncertain significance (Mar 06, 2025)
15-40458933-C-T		not specified	Uncertain significance (Jan 29, 2025)
15-40458939-C-T		not specified	Uncertain significance (Feb 22, 2025)
15-40458973-G-A		not specified	Uncertain significance (May 23, 2024)
15-40458979-G-A		not specified	Uncertain significance (Jan 23, 2025)
15-40459005-C-T		not specified	Uncertain significance (Oct 25, 2022)
15-40459006-G-A		not specified	Uncertain significance (Dec 13, 2021)
15-40459042-C-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BAHD1	protein_coding	protein_coding	ENST00000416165	6	28522

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.985	0.0145	125624	0	118	125742	0.000469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	435	519	0.838	0.0000344	4947
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00147	0.00147
Ashkenazi Jewish	0.00	0.00
East Asian	0.000817	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000817	0.000816
South Asian	0.00190	0.00190
Other	0.000493	0.000489

dbNSFP

Source: dbNSFP

• 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

Haploinsufficiency Scores

• pHI: 0.185
• hipred: Y
• hipred_score: 0.572
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bahd1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; limbs/digits/tail phenotype

Gene ontology

• Biological process: heterochromatin assembly;negative regulation of transcription, DNA-templated
• Cellular component: nucleoplasm;chromatin silencing complex;chromosome
• Molecular function: chromatin binding;protein binding