PBRM1

polybromo 1, the group of Bromodomain containing|PBAF complex

Basic information

Region (hg38): 3:52545351-52685917

Links

ENSG00000163939 ∙ NCBI:55193 ∙ OMIM:606083 ∙ HGNC:30064 ∙ Uniprot:Q86U86 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Clear cell renal cell carcinoma	AD	Oncologic	Variants have been described as segregating with clear cell renal cell carcinoma, and awareness may be beneficial for surveillance to allow early diagnosis and management	Oncologic	25911086

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PBRM1 gene.

• not provided (54 variants)
• not specified (8 variants)
• PBRM1-related BAFopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PBRM1 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1	2	4
non coding					48	48
Total	0	0	1	1	49

Variants in PBRM1

This is a list of pathogenic ClinVar variants found in the PBRM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-52548224-C-T		not specified	not provided (Sep 19, 2013)
3-52548429-A-AT			Benign (Aug 15, 2019)
3-52550218-AAAAAC-A			Benign (Jun 23, 2018)
3-52550462-G-A		not specified	not provided (Sep 19, 2013)
3-52550571-G-A			Uncertain significance (Nov 01, 2016)
3-52550699-A-G			Benign (Jun 22, 2018)
3-52554639-G-A			Benign (Jun 23, 2018)
3-52562157-TA-T			Benign (Aug 15, 2019)
3-52563056-TTAAATTATTAATGGTATTAATA-T			Benign (Jun 23, 2018)
3-52563363-CCTCACTAT-C		Clear cell carcinoma of kidney	Pathogenic (Jun 01, 2015)
3-52563415-C-A			Uncertain significance (Feb 08, 2023)
3-52563648-G-A			Benign (Jun 22, 2018)
3-52564343-T-C			Benign (Jun 23, 2018)
3-52564524-G-A			Benign (Jun 19, 2021)
3-52576399-T-C			Benign (Jun 22, 2018)
3-52576497-T-C			Benign (Jun 23, 2018)
3-52586698-G-T			Benign (Jun 22, 2018)
3-52586729-G-A			Benign (Jun 23, 2018)
3-52587570-C-CT			Benign (Aug 15, 2019)
3-52587611-C-T			Benign (Jun 22, 2018)
3-52587806-T-TTTC			Benign (Jun 19, 2021)
3-52587823-C-T			Benign (Jun 19, 2021)
3-52589219-C-A		not specified	not provided (Sep 19, 2013)
3-52589449-A-T			Benign (Jun 22, 2018)
3-52603423-T-C			Benign (Jun 23, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PBRM1	protein_coding	protein_coding	ENST00000394830	29	140566

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.20e-10	125673	0	22	125695	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.84	534	849	0.629	0.0000447	10483
Missense in Polyphen		54	133.54	0.40437		1539
Synonymous	1.44	259	290	0.893	0.0000148	2863
Loss of Function	7.84	5	81.3	0.0615	0.00000468	1012

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000418	0.000401
Ashkenazi Jewish	0.000113	0.0000992
East Asian	0.000196	0.000109
Finnish	0.000171	0.0000924
European (Non-Finnish)	0.0000694	0.0000528
Middle Eastern	0.000196	0.000109
South Asian	0.000199	0.000131
Other	0.000195	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Required for the stability of the SWI/SNF chromatin remodeling complex SWI/SNF-B (PBAF). Acts as a negative regulator of cell proliferation. {ECO:0000269|PubMed:21248752, ECO:0000303|PubMed:22952240, ECO:0000303|PubMed:26601204}.
• Pathway: Hepatocellular carcinoma - Homo sapiens (human);Pathways in clear cell renal cell carcinoma;Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;Generic Transcription Pathway;RNA Polymerase II Transcription;RMTs methylate histone arginines;Chromatin modifying enzymes;Chromatin organization;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.241

Intolerance Scores

• loftool: 0.0745
• rvis_EVS: -2.15
• rvis_percentile_EVS: 1.48

Haploinsufficiency Scores

• pHI: 0.904
• hipred: Y
• hipred_score: 0.768
• ghis: 0.709

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pbrm1
• Phenotype: immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; embryo phenotype

Gene ontology

• Biological process: mitotic cell cycle;nucleosome disassembly;chromatin remodeling;transcription elongation from RNA polymerase II promoter;negative regulation of cell population proliferation;ATP-dependent chromatin remodeling
• Cellular component: nuclear chromosome;nucleoplasm;RSC-type complex
• Molecular function: DNA binding;chromatin binding;protein binding;DNA translocase activity