BUD13

BUD13 homolog, the group of Spliceosomal P complex|NTC associated proteins

Basic information

Region (hg38): 11:116748170-116772987

Links

ENSG00000137656 ∙ NCBI:84811 ∙ ∙ HGNC:28199 ∙ Uniprot:Q9BRD0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• progeroid syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BUD13 gene.

• not_specified (113 variants)
• not_provided (1 variants)
• Gait_ataxia (1 variants)
• Achalasia-progeroid_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BUD13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032725.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			102	10	1	113
nonsense	1					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	102	11	1

Highest pathogenic variant AF is 0.00000495673

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BUD13	protein_coding	protein_coding	ENST00000260210	10	24819

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000206	0.995	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.210	371	360	1.03	0.0000203	4039
Missense in Polyphen		88	99.841	0.8814		1123
Synonymous	-0.220	128	125	1.02	0.00000629	1220
Loss of Function	2.49	14	28.3	0.495	0.00000161	326

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000572	0.000572
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000274	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000205	0.000202
Middle Eastern	0.000274	0.000272
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0730

Intolerance Scores

• loftool: 0.861
• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.21

Haploinsufficiency Scores

• pHI: 0.209
• hipred: Y
• hipred_score: 0.728
• ghis: 0.511

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0811

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bud13

Gene ontology

• Biological process: mRNA splicing, via spliceosome
• Cellular component: nucleus;U2-type spliceosomal complex;RES complex
• Molecular function: RNA binding;protein binding