BUD13

Chr 11AR

BUD13 spliceosome associated protein

Also known as: ACHPS, Cwc26, fSAP71

NCBI Gene: 84811ENSG00000137656UniProt: Q9BRD0OMIM: 620691

The BUD13 protein is a component of the spliceosome that enables RNA binding and is involved in pre-mRNA splicing, including splicing of U12-type introns as part of the minor spliceosome. Mutations cause autosomal recessive intellectual disability with microcephaly and seizures, typically presenting in early childhood. The gene shows minimal constraint against loss-of-function variants (pLI near 0), consistent with recessive inheritance where heterozygous carriers are unaffected.

OMIMResearchSummary from RefSeq, UniProt
DNmechanismARLOEUF 0.771 OMIM phenotype
Clinical Summary— BUD13
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
3 unique Pathogenic / Likely Pathogenic· 74 VUS of 100 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.77LOEUF
pLI 0.000
Z-score 2.49
OE 0.49 (0.33–0.77)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
-0.21Z-score
OE missense 1.03 (0.95–1.12)
371 obs / 359.8 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.49 (0.33–0.77)
0≤0.351.4
Missense OE1.03 (0.95–1.12)
0≤0.61.4
Synonymous OE1.02
0≤1.21.6
LoF obs/exp: 14 / 28.3Missense obs/exp: 371 / 359.8Syn Z: -0.22
DN
0.77top 25%
GOF
0.5268th %ile
LOF
0.3842th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

100 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic3
VUS74
Likely Benign9
Conflicting1
3
Pathogenic
74
VUS
9
Likely Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
0
2
0
3
Likely Pathogenic
0
0
0
0
0
VUS
0
72
2
0
74
Likely Benign
0
8
0
1
9
Benign
0
0
0
0
0
Conflicting
—1
Total1804187

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

View in ClinVar →

Protein Context — Lollipop Plot

BUD13 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 4 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients