BUD23

BUD23 rRNA methyltransferase and ribosome maturation factor, the group of Ribosomal biogenesis factors|7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 7:73683596-73698212

Previous symbols: [ "WBSCR22" ]

Links

ENSG00000071462 ∙ NCBI:114049 ∙ OMIM:615733 ∙ HGNC:16405 ∙ Uniprot:O43709 ∙ 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 BUD23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BUD23 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	22	1	1

Variants in BUD23

This is a list of pathogenic ClinVar variants found in the BUD23 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-73683630-C-T		not specified	Uncertain significance (Jan 22, 2024)
7-73683631-G-A			Likely benign (Jan 01, 2023)
7-73683633-C-T		not specified	Uncertain significance (May 14, 2024)
7-73683635-C-T		not specified	Uncertain significance (May 06, 2024)
7-73683638-G-A		not specified	Uncertain significance (Feb 11, 2022)
7-73683644-C-T		not specified	Uncertain significance (Jun 01, 2023)
7-73683656-G-A		not specified	Uncertain significance (May 13, 2024)
7-73683789-G-A		not specified	Conflicting classifications of pathogenicity (Aug 01, 2023)
7-73686706-A-G		not specified	Uncertain significance (Dec 14, 2023)
7-73686823-G-A		not specified	Uncertain significance (Jul 14, 2022)
7-73686881-T-A		not specified	Uncertain significance (Apr 08, 2022)
7-73686886-G-C		not specified	Uncertain significance (May 20, 2024)
7-73687014-G-T		not specified	Uncertain significance (Aug 02, 2021)
7-73687093-C-G		not specified	Uncertain significance (May 11, 2022)
7-73690954-A-G		not specified	Uncertain significance (Apr 08, 2022)
7-73692599-C-T		not specified	Uncertain significance (Dec 18, 2023)
7-73693332-G-A		not specified	Uncertain significance (Jan 03, 2024)
7-73693403-C-T			Benign (Dec 14, 2017)
7-73694021-A-C		not specified	Uncertain significance (Feb 03, 2022)
7-73694032-C-T		not specified	Uncertain significance (Apr 11, 2023)
7-73694041-C-T		not specified	Uncertain significance (Jun 03, 2022)
7-73697498-G-A		not specified	Uncertain significance (Feb 12, 2024)
7-73697627-C-T		not specified	Uncertain significance (Aug 16, 2022)
7-73697628-G-C		not specified	Uncertain significance (Sep 26, 2022)
7-73697631-G-A		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BUD23	protein_coding	protein_coding	ENST00000423497	13	22137

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000766	0.996	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.271	170	180	0.943	0.0000100	1919
Missense in Polyphen		72	78.301	0.91953		783
Synonymous	-0.0200	64	63.8	1.00	0.00000308	578
Loss of Function	2.56	11	24.7	0.445	0.00000149	246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000271	0.000271
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000218	0.000217
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000218	0.000217
South Asian	0.000523	0.000523
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that specifically methylates the N(7) position of a guanine in 18S rRNA (PubMed:25851604). Requires the methyltransferase adapter protein TRM112 for full rRNA methyltransferase activity (PubMed:25851604). Involved in the pre-rRNA processing steps leading to small-subunit rRNA production independently of its RNA-modifying catalytic activity (PubMed:25851604). Important for biogenesis end export of the 40S ribosomal subunit independent on its methyltransferase activity (PubMed:24086612). Locus-specific steroid receptor coactivator. Potentiates transactivation by glucocorticoid (NR3C1), mineralocorticoid (NR3C2), androgen (AR) and progesterone (PGR) receptors (PubMed:24488492). Required for the maintenance of open chromatin at the TSC22D3/GILZ locus to facilitate NR3C1 loading on the response elements (PubMed:24488492). Required for maintenance of dimethylation on histone H3 'Lys-79' (H3K79me2), although direct histone methyltransferase activity is not observed in vitro (PubMed:24488492). {ECO:0000250, ECO:0000269|PubMed:24086612, ECO:0000269|PubMed:24488492, ECO:0000269|PubMed:25851604}.
• Disease: DISEASE: Note=BUD23 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. Haploinsufficiency of BUD23 may be the cause of certain cardiovascular and musculo-skeletal abnormalities observed in the disease. {ECO:0000305|PubMed:11978965}.
• Pathway: rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.0575
• hipred: N
• hipred_score: 0.432
• ghis: 0.511

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Bud23

Gene ontology

• Biological process: chromatin organization;rRNA (guanine-N7)-methylation;positive regulation of rRNA processing
• Cellular component: nucleus;nucleoplasm;nucleolus;perinuclear region of cytoplasm
• Molecular function: RNA binding;methyltransferase activity;rRNA (guanine) methyltransferase activity;protein heterodimerization activity