MYBBP1A

MYB binding protein 1a, the group of B-WICH chromatin-remodelling complex subunits|Armadillo like helical domain containing

Basic information

Region (hg38): 17:4538897-4555386

Links

ENSG00000132382 ∙ NCBI:10514 ∙ OMIM:604885 ∙ HGNC:7546 ∙ Uniprot:Q9BQG0 ∙ 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 MYBBP1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYBBP1A 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				6	6	12
missense			133	17	9	159
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	2	4
non coding						0
Total	0	0	133	23	16

Variants in MYBBP1A

This is a list of pathogenic ClinVar variants found in the MYBBP1A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4539503-G-A		not specified	Uncertain significance (Oct 10, 2023)
17-4539506-T-C			Benign (Dec 31, 2019)
17-4539513-G-A		not specified	Uncertain significance (Jul 08, 2022)
17-4539525-A-G		not specified	Uncertain significance (Jun 19, 2024)
17-4539566-T-C		not specified	Uncertain significance (Aug 28, 2024)
17-4539596-G-A		not specified	Uncertain significance (Nov 25, 2024)
17-4539606-C-T		not specified	Likely benign (Apr 26, 2024)
17-4539613-T-A			Likely benign (Dec 01, 2022)
17-4539629-G-A		not specified	Likely benign (May 16, 2022)
17-4539636-G-A			Benign (Dec 31, 2019)
17-4539639-T-C		not specified	Uncertain significance (Dec 10, 2024)
17-4539683-C-G		not specified	Uncertain significance (Sep 01, 2021)
17-4539684-G-A		not specified	Uncertain significance (Oct 14, 2023)
17-4539689-G-A		not specified	Uncertain significance (Feb 23, 2023)
17-4539692-G-A		not specified	Uncertain significance (Aug 02, 2021)
17-4539704-G-A		not specified	Uncertain significance (Apr 08, 2024)
17-4539716-G-T		not specified	Uncertain significance (Aug 14, 2024)
17-4539726-C-T		not specified	Uncertain significance (Jun 03, 2024)
17-4539737-G-A		not specified	Uncertain significance (Jun 03, 2024)
17-4539758-C-T		not specified	Likely benign (Jul 19, 2022)
17-4539761-T-C		not specified	Uncertain significance (Dec 18, 2023)
17-4539769-C-G		not specified	Uncertain significance (May 27, 2022)
17-4539776-C-T		not specified	Uncertain significance (Dec 18, 2023)
17-4539815-G-A		not specified	Uncertain significance (Mar 06, 2023)
17-4539823-C-G		MYBBP1A-related condition	Uncertain significance (Apr 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYBBP1A	protein_coding	protein_coding	ENST00000381556	27	16735

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.23e-42	0.00000156	125298	3	447	125748	0.00179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.75	1022	803	1.27	0.0000512	8550
Missense in Polyphen		300	243.15	1.2338		2778
Synonymous	-5.57	479	347	1.38	0.0000221	2696
Loss of Function	0.154	64	65.3	0.979	0.00000321	732

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0108	0.0107
Ashkenazi Jewish	0.000794	0.000794
East Asian	0.000875	0.000870
Finnish	0.000343	0.000323
European (Non-Finnish)	0.000946	0.000888
Middle Eastern	0.000875	0.000870
South Asian	0.00350	0.00347
Other	0.00221	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May activate or repress transcription via interactions with sequence specific DNA-binding proteins (By similarity). Repression may be mediated at least in part by histone deacetylase activity (HDAC activity) (By similarity). Acts as a corepressor and in concert with CRY1, represses the transcription of the core circadian clock component PER2 (By similarity). Preferentially binds to dimethylated histone H3 'Lys-9' (H3K9me2) on the PER2 promoter (By similarity). Has a role in rRNA biogenesis together with PWP1 (PubMed:29065309). {ECO:0000250|UniProtKB:Q7TPV4, ECO:0000269|PubMed:29065309}.
• Pathway: Energy Metabolism;B-WICH complex positively regulates rRNA expression;Positive epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription) (Consensus)

Recessive Scores

• pRec: 0.230

Intolerance Scores

• loftool: 0.961
• rvis_EVS: 2.3
• rvis_percentile_EVS: 98.33

Haploinsufficiency Scores

• pHI: 0.606
• hipred: Y
• hipred_score: 0.566
• ghis: 0.474

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.765

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mybbp1a
• Phenotype: embryo 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); 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)

Zebrafish Information Network

• Gene name: mybbp1a
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: necrotic

Gene ontology

• Biological process: osteoblast differentiation;regulation of transcription, DNA-templated;respiratory electron transport chain;circadian regulation of gene expression;cellular response to glucose starvation;ribosome biogenesis;positive regulation of gene expression, epigenetic;negative regulation of transcription, DNA-templated;positive regulation of cell cycle arrest;intrinsic apoptotic signaling pathway by p53 class mediator;positive regulation of anoikis
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;membrane;NLS-dependent protein nuclear import complex;intracellular membrane-bounded organelle
• Molecular function: transcription corepressor activity;RNA binding;transcription factor binding;sequence-specific DNA binding;E-box binding