BUD23

Chr 7

BUD23 rRNA methyltransferase and ribosome maturation factor

Also known as: HASJ4442, HUSSY-3, MERM1, PP3381, WBMT, WBSCR22

NCBI Gene: 114049 ENSG00000071462 UniProt: O43709 OMIM: 615733

This gene encodes a methyltransferase that methylates 18S ribosomal RNA and is essential for ribosome biogenesis and nuclear export of the 40S ribosomal subunit. BUD23 is deleted in Williams syndrome, a multisystem developmental disorder caused by contiguous gene deletions at chromosome 7q11.23. The gene shows high constraint against loss-of-function variants (pLI ~1.0, LOEUF 0.736), indicating that heterozygous loss is likely not tolerated in the general population.

OMIM ResearchSummary from RefSeq, UniProt

This gene encodes a protein containing a nuclear localization signal and an S-adenosyl-L-methionine binding motif typical of methyltransferases, suggesting that the encoded protein may act on DNA methylation. This gene is deleted in Williams syndrome, a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.23. Alternatively spliced transcript variants have been found. [provided by RefSeq, Feb 2011]

OMIM ResearchGenerating clinical summary…

LOEUF 0.74

Clinical Summary— BUD23

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

48 VUS of 90 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.74LOEUF

pLI 0.000

Z-score 2.56

OE 0.44 (0.28–0.74)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.27Z-score

OE missense 0.94 (0.83–1.07)

170 obs / 180.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.44 (0.28–0.74)

0≤0.351.4

Missense OE?0.94 (0.83–1.07)

0≤0.61.4

Synonymous OE?1.00

0≤1.21.6

LoF obs/exp: 11 / 24.7Missense obs/exp: 170 / 180.2Syn Z: -0.02

ClinVar Variant Classifications

90 submitted variants in ClinVar

ClinVar

Classification Summary

VUS48

Likely Benign3

Benign1

Conflicting1

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	0	0	0	0
VUS	0	48	0	0	48
Likely Benign	0	2	0	1	3
Benign	0	0	0	1	1
Conflicting	—				1
Total	0	50	0	2	53

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

164 pathogenic / likely-pathogenic (of 168) ClinVar copy-number / structural variants overlap BUD23 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →