BRDT

bromodomain testis associated, the group of Bromodomain containing|Bromodomain and extra-terminal domain family

Basic information

Region (hg38): 1:91949343-92014426

Links

ENSG00000137948 ∙ NCBI:676 ∙ OMIM:602144 ∙ HGNC:1105 ∙ Uniprot:Q58F21 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 21 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 21	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	28199965

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BRDT gene.

• Premature ovarian failure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRDT 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				1	1	2
missense			45	1		46
nonsense						0
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	1	0	45	2	1

Variants in BRDT

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

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

Position	Type	Phenotype	Significance	ClinVar
1-91962764-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-91962854-T-C		not specified	Uncertain significance (Nov 07, 2024)
1-91964646-A-C		not specified	Uncertain significance (May 11, 2022)
1-91964648-A-T		not specified	Uncertain significance (Jul 19, 2023)
1-91964709-C-T		not specified	Uncertain significance (Jul 02, 2024)
1-91964728-C-A		not specified	Uncertain significance (Mar 22, 2023)
1-91968164-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-91976410-T-G		not specified	Uncertain significance (Dec 01, 2023)
1-91977043-G-A		not specified	Uncertain significance (Oct 03, 2023)
1-91977137-A-T		not specified	Uncertain significance (Jun 05, 2023)
1-91977157-A-T		not specified	Uncertain significance (Jun 17, 2022)
1-91977245-G-A		BRDT-related disorder	Likely benign (Aug 28, 2019)
1-91977263-T-C		not specified	Uncertain significance (Nov 16, 2021)
1-91977273-G-C		not specified	Uncertain significance (Sep 27, 2024)
1-91977287-A-C		not specified	Uncertain significance (Aug 16, 2022)
1-91977328-A-C		not specified	Uncertain significance (Jul 11, 2023)
1-91977379-C-A		not specified	Uncertain significance (May 04, 2022)
1-91978178-A-G		not specified	Uncertain significance (Jan 16, 2024)
1-91978201-T-A		not specified	Uncertain significance (May 31, 2023)
1-91978216-G-C		not specified	Uncertain significance (Aug 03, 2022)
1-91978246-A-G		not specified	Uncertain significance (Nov 19, 2024)
1-91978277-C-T		not specified	Uncertain significance (Jul 25, 2024)
1-91979599-C-A		not specified	Uncertain significance (Mar 22, 2023)
1-91979600-C-G		not specified	Uncertain significance (May 31, 2023)
1-91979603-T-C		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRDT	protein_coding	protein_coding	ENST00000362005	18	65056

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.76e-9	1.00	125686	0	58	125744	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.457	437	465	0.940	0.0000230	6268
Missense in Polyphen		87	109.53	0.7943		1509
Synonymous	-0.367	167	161	1.04	0.00000829	1668
Loss of Function	3.46	22	47.8	0.460	0.00000239	649

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000767	0.000760
Ashkenazi Jewish	0.00	0.00
East Asian	0.000609	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000137	0.000132
Middle Eastern	0.000609	0.000598
South Asian	0.000373	0.000359
Other	0.000549	0.000489

dbNSFP

Source: dbNSFP

• Function: 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 spermatocytes: plays a role in meiotic and post-meiotic cells by binding to acetylated histones at the promoter of specific meiotic and post-meiotic genes, facilitating their activation at the appropriate time (PubMed:22901802). In the post-meiotic phase of spermatogenesis, binds to hyperacetylated histones and participates in their general removal from DNA (PubMed:22901802). Also recognizes and binds a subset of butyrylated histones: able to bind histone H4 butyrylated at 'Lys-8' (H4K8ac), while it is not able to bind H4 butyrylated at 'Lys-5' (H4K5ac) (By similarity). Also acts as a component of the splicing machinery in pachytene spermatocytes and round spermatids and participates in 3'-UTR truncation of specific mRNAs in post-meiotic spermatids (By similarity). Required for chromocenter organization, a structure comprised of peri-centromeric heterochromatin. {ECO:0000250|UniProtKB:Q91Y44, ECO:0000269|PubMed:15647849, ECO:0000269|PubMed:22464331, ECO:0000269|PubMed:22901802, ECO:0000269|PubMed:9367677}.
• Disease: DISEASE: Spermatogenic failure 21 (SPGF21) [MIM:617644]: An infertility disorder caused by spermatogenesis defects and characterized by acephalic spermatozoa in the semen of affected individuals. SPGF21 inheritance is autosomal recessive. {ECO:0000269|PubMed:28199965}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Chemical Compounds to monitor Proteins (Consensus)

Recessive Scores

• pRec: 0.305

Intolerance Scores

• loftool: 0.932
• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.26

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0431

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Brdt
• Phenotype: skeleton phenotype; reproductive system phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: histone displacement;chromatin remodeling;regulation of transcription, DNA-templated;mRNA processing;male meiotic nuclear division;male meiosis I;spermatogenesis;RNA splicing;cell differentiation;regulation of RNA splicing;positive regulation of transcription involved in meiotic cell cycle
• Cellular component: nucleus
• Molecular function: transcription coactivator activity;histone binding;lysine-acetylated histone binding