BRDT (bromodomain testis associated)

Gene

• Entrez ID: 676
• Gene name: Bromodomain testis associated
• Gene symbol: BRDT
• Synonyms (NCBI Gene): BRD6, CT9, SPGF21
• Chromosome: 1
• Chromosome location: 1p22.1
• Summary: BRDT is similar to the RING3 protein family. It possesses 2 bromodomain motifs and a PEST sequence (a cluster of proline, glutamic acid, serine, and threonine residues), characteristic of proteins that undergo rapid intracellular degradation. The bromodom

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs754258809	G>A	Pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT023817	hsa-miR-1-3p	Microarray	18668037
MIRT029810	hsa-miR-26b-5p	Microarray	19088304

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	IBA
GO:0003682	Function	Chromatin binding	IBA
GO:0003713	Function	Transcription coactivator activity	TAS	10365964
GO:0004674	Function	Protein serine/threonine kinase activity	IBA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	25593309
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	ISS
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IBA
GO:0006338	Process	Chromatin remodeling	IEA
GO:0006338	Process	Chromatin remodeling	ISS
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IMP	28199965
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006397	Process	MRNA processing	IEA
GO:0007140	Process	Male meiotic nuclear division	IEA
GO:0007140	Process	Male meiotic nuclear division	ISS
GO:0007141	Process	Male meiosis I	IEA
GO:0007141	Process	Male meiosis I	ISS
GO:0007283	Process	Spermatogenesis	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0010628	Process	Positive regulation of gene expression	IEA
GO:0010628	Process	Positive regulation of gene expression	ISS
GO:0030154	Process	Cell differentiation	IEA
GO:0030674	Function	Protein-macromolecule adaptor activity	IEA
GO:0035092	Process	Sperm DNA condensation	IEA
GO:0035092	Process	Sperm DNA condensation	ISS
GO:0042393	Function	Histone binding	IBA
GO:0042393	Function	Histone binding	IDA	22464331
GO:0042393	Function	Histone binding	IEA
GO:0043484	Process	Regulation of RNA splicing	IEA
GO:0043484	Process	Regulation of RNA splicing	ISS
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0051321	Process	Meiotic cell cycle	IEA
GO:0140008	Function	Histone H4 reader activity	IEA

Other IDs

• MIM: 602144
• HGNC: 1105
• e!Ensembl: ENSG00000137948

Protein

• UniProt ID: Q58F21
• Protein name: Bromodomain testis-specific protein (Cancer/testis antigen 9) (CT9) (RING3-like protein)
• Protein function: Testis-specific chromatin protein that specifically binds histone H4 acetylated at 'Lys-5' and 'Lys-8' (H4K5ac and H4K8ac, respectively) and plays a key role in spermatogenesis (PubMed:22464331, PubMed:22901802). Required in late pachytene sperm
• PDB: 2RFJ, 4FLP, 4KCX, 5VBQ, 5VBR, 7BJY, 7L73, 7L99, 7L9A, 7LEJ, 7LEK, 7LEL, 7LEM, 7MRC, 7MRD, 7MRG, 7MRH, 7UBO, 7UUU, 8CZA, 8YHS
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00439	Bromodomain	35 → 121	Bromodomain	Domain
  PF00439	Bromodomain	276 → 364	Bromodomain	Domain
  PF17035	BET	509 → 573	Bromodomain extra-terminal - transcription regulation	Domain
  PF17105	BRD4_CDT	904 → 947	C-terminal domain of bromodomain protein 4	Family

• Tissue specificity: TISSUE SPECIFICITY: Testis-specific. A 3-fold higher expression is seen in adult testis than in embryo testis. Expression seems to be correlated with histone H4 hyperacetylation during the haploid phase of spermatogenesis (spermiogenesis). No expression,
• Sequence:

  MSLPSRQTAIIVNPPPPEYINTKKNGRLTNQLQYLQKVVLKDLWKHSFSWPFQRPVDAVK
  LQLPDYYTIIKNPMDLNTIKKRLENKYYAKASECIEDFNTMFSNCYLYNKPGDDIVLMAQ
  ALEKLFMQKLSQMPQEEQVVGVKERIKKGTQQNIAVSSAKEKSSPSATEKVFKQQEIPSV
  FPKTSISPLNVVQGASVNSSSQTAAQVTKGVKRKADTTTPATSAVKASSEFSPTFTEKSV
  ALPPIKENMPKNVLPDSQQQYNVVKTVKVTEQLRHCSEILKEMLAKKHFSYAWPFYNPVD
  VNALGLHNYYDVVKNPMDLGTIKEKMDNQEYKDAYKFAADVRLMFMNCYKYNPPDHEVVT
  MARMLQDVFETHFSKIPIEPVESMPLCYIKTDITETTGRENTNEASSEGNSSDDSEDERV
  KRLAKLQEQLKAVHQQLQVLSQVPFRKLNKKKEKSKKEKKKEKVNNSNENPRKMCEQMRL
  KEKSKRNQPKKRKQQFIGLKSEDEDNAKPMNYDEKRQLSLNINKLPGDKLGRVVHIIQSR
  EPSLSNSNPDEIEIDFETLKASTLRELEKYVSACLRKRPLKPPAKKIMMSKEELHSQKKQ
  ELEKRLLDVNNQLNSRKRQTKSDKTQPSKAVENVSRLSESSSSSSSSSESESSSSDLSSS
  DSSDSESEMFPKFTEVKPNDSPSKENVKKMKNECIPPEGRTGVTQIGYCVQDTTSANTTL
  VHQTTPSHVMPPNHHQLAFNYQELEHLQTVKNISPLQILPPSGDSEQLSNGITVMHPSGD
  SDTTMLESECQAPVQKDIKIKNADSWKSLGKPVKPSGVMKSSDELFNQFRKAAIEKEVKA
  RTQELIRKHLEQNTKELKASQENQRDLGNGLTVESFSNKIQNKCSGEEQKEHQQSSEAQD
  KSKLWLLKDRDLARQKEQERRRREAMVGTIDMTLQSDIMTMFENNFD

• Sequence length: 947

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Premature ovarian failure	Pathogenic	rs1188709614	RCV001270186	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AZOOSPERMIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BRDT-related disorder	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN FAILURE, PREMATURE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spermatogenic failure 21	Uncertain significance	ClinVar ClinVar, Disgenet, GWAS catalog, HPO ClinVar, Disgenet, GWAS catalog, HPO ClinVar, Disgenet, GWAS catalog, HPO	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acephalic spermatozoa	Acephalic spermatozoa	BEFREE	28199965		★☆☆☆☆ Found in Text Mining only
Acephalic spermatozoa	Acephalic spermatozoa	HPO_DG			★☆☆☆☆ Found in Text Mining only
Adenocarcinoma	Adenocarcinoma	BEFREE	15826242		★☆☆☆☆ Found in Text Mining only
Asthenozoospermia	Asthenozoospermia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	10704737, 28580303		★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	33658703	Associate	★☆☆☆☆ Found in Text Mining only
Gastric Adenocarcinoma	Gastric Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of brain	Brain Neoplasms	BEFREE	29764999		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	10704737, 28580303		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	23543289		★☆☆☆☆ Found in Text Mining only
Non-obstructive azoospermia	Non-obstructive azoospermia	BEFREE	25374327		★☆☆☆☆ Found in Text Mining only
SPERMATOGENIC FAILURE 21	Spermatogenic Failure	UNIPROT_DG	28199965		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Squamous cell carcinoma	Carcinoma	BEFREE	15826242		★☆☆☆☆ Found in Text Mining only
Subfertility	Subfertility	BEFREE	20538714		★☆☆☆☆ Found in Text Mining only
Teratozoospermia	Teratozoospermia	BEFREE	24865796		★☆☆☆☆ Found in Text Mining only