BDP1

B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB, the group of Myb/SANT domain containing|General transcription factor IIIB complex subunits

Basic information

Region (hg38): 5:71455650-71567820

Previous symbols: [ "TFNR", "TAF3B1" ]

Links

ENSG00000145734 ∙ NCBI:55814 ∙ OMIM:607012 ∙ HGNC:13652 ∙ Uniprot:A6H8Y1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hearing loss, autosomal recessive 112 (Limited), mode of inheritance: AR
• hearing loss, autosomal recessive 112 (Limited), mode of inheritance: AR
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• nonsyndromic genetic hearing loss (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 112	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	Audiologic/Otolaryngologic	24312468
Hearing loss has been described as postlingual

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BDP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BDP1 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				32	11	43
missense			111	35	30	176
nonsense						0
start loss						0
frameshift			1			1
inframe indel			1	1		2
splice donor/acceptor (+/-2bp)			2		1	3
splice region				5	3	8
non coding			1	66	87	154
Total	0	0	116	134	129

Variants in BDP1

This is a list of pathogenic ClinVar variants found in the BDP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-71455798-A-T			Likely benign (Jun 29, 2018)
5-71455906-A-G			Uncertain significance (Aug 16, 2022)
5-71455954-A-G			Benign (Apr 07, 2020)
5-71455991-T-G		not specified • Hearing loss, autosomal recessive 112	Benign (Jul 14, 2021)
5-71456042-A-G			Likely benign (Jul 20, 2020)
5-71456065-C-T		not specified	Uncertain significance (Nov 15, 2021)
5-71456070-G-A			Likely benign (Apr 13, 2018)
5-71458335-G-C			Benign (Nov 10, 2018)
5-71458581-C-T		not specified	Uncertain significance (Jan 08, 2024)
5-71458621-T-G		not specified	Uncertain significance (Jan 23, 2024)
5-71458648-A-T			Benign (Jul 17, 2019)
5-71458662-C-T			Uncertain significance (Dec 07, 2022)
5-71458710-C-T		not specified	Uncertain significance (Apr 05, 2023)
5-71458727-A-G		not specified	Likely benign (Jan 22, 2024)
5-71458740-C-T			Benign (May 24, 2018)
5-71458756-C-T			Likely benign (Oct 17, 2019)
5-71461883-A-G		not specified	Uncertain significance (Apr 09, 2024)
5-71461934-A-G			Likely benign (Mar 13, 2018)
5-71461958-CT-C			Benign (Nov 13, 2019)
5-71461958-CTT-C			Benign (Feb 06, 2020)
5-71461958-CTTT-C			Likely benign (Nov 13, 2019)
5-71461958-C-CT			Benign (Aug 15, 2019)
5-71461958-C-CTT			Benign (Sep 17, 2019)
5-71461958-C-CTTT			Likely benign (Sep 27, 2019)
5-71461958-C-CTTTTT			Likely benign (Feb 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BDP1	protein_coding	protein_coding	ENST00000358731	39	112208

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.33e-21	1.00	124706	0	88	124794	0.000353

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.124	1314	1.30e+3	1.01	0.0000624	17220
Missense in Polyphen		324	365.95	0.88536		5029
Synonymous	-1.25	482	448	1.08	0.0000225	4917
Loss of Function	5.22	55	116	0.476	0.00000601	1614

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00109	0.00107
Ashkenazi Jewish	0.00	0.00
East Asian	0.000227	0.000223
Finnish	0.000233	0.000232
European (Non-Finnish)	0.000378	0.000371
Middle Eastern	0.000227	0.000223
South Asian	0.000273	0.000261
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: General activator of RNA polymerase III transcription. Requires for transcription from all three types of polymerase III promoters. Requires for transcription of genes with internal promoter elements and with promoter elements upstream of the initiation site. {ECO:0000269|PubMed:11040218}.
• Pathway: Gene expression (Transcription);rna polymerase iii transcription;RNA Polymerase III Abortive And Retractive Initiation;RNA Polymerase III Transcription Initiation From Type 1 Promoter;RNA Polymerase III Transcription Initiation From Type 2 Promoter;RNA Polymerase III Transcription Initiation From Type 3 Promoter;RNA Polymerase III Transcription Initiation;RNA Polymerase III Transcription (Consensus)

Recessive Scores

• pRec: 0.0695

Intolerance Scores

• loftool: 0.904
• rvis_EVS: 2.39
• rvis_percentile_EVS: 98.48

Haploinsufficiency Scores

• pHI: 0.235
• hipred: N
• hipred_score: 0.478
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bdp1

Gene ontology

• Biological process: RNA polymerase III preinitiation complex assembly
• Cellular component: transcription factor TFIIIB complex;nucleoplasm
• Molecular function: RNA polymerase III general transcription initiation factor activity;TFIIIC-class transcription factor complex binding;DNA binding