BUD13

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

Basic information

Region (hg38): 11:116748169-116772987

Links

ENSG00000137656 ∙ NCBI:84811 ∙ ∙ HGNC:28199 ∙ Uniprot:Q9BRD0 ∙ 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 BUD13 gene.

• Inborn genetic diseases (43 variants)
• not provided (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.

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						0
missense			39	4	1	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	4	1

Variants in BUD13

This is a list of pathogenic ClinVar variants found in the BUD13 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-116748553-G-A		not specified	Uncertain significance (Apr 28, 2022)
11-116757184-A-C		not specified	Uncertain significance (Oct 20, 2023)
11-116757203-G-A		not specified	Uncertain significance (Nov 09, 2023)
11-116757212-C-G		not specified	Uncertain significance (Jan 18, 2023)
11-116757213-T-C		not specified	Uncertain significance (Jul 12, 2023)
11-116757772-T-C		not specified	Uncertain significance (Dec 27, 2023)
11-116757775-T-C		not specified	Uncertain significance (Oct 26, 2022)
11-116757907-T-C		not specified	Likely benign (Jun 11, 2021)
11-116757915-T-A		not specified	Uncertain significance (Apr 25, 2023)
11-116757927-T-G		not specified	Uncertain significance (Sep 06, 2022)
11-116757936-C-T		not specified	Uncertain significance (Jan 22, 2024)
11-116758312-T-C		not specified	Uncertain significance (Aug 12, 2021)
11-116758326-C-A		not specified	Uncertain significance (Dec 17, 2023)
11-116758363-G-A		not specified	Uncertain significance (Jun 24, 2022)
11-116759124-C-T		not specified	Uncertain significance (Jul 12, 2022)
11-116759163-G-C		not specified	Uncertain significance (Jun 21, 2021)
11-116760753-A-T		not specified	Uncertain significance (Mar 25, 2022)
11-116760826-G-C			Benign (Jun 29, 2018)
11-116760899-T-C		not specified	Uncertain significance (Jun 01, 2023)
11-116762581-A-C		not specified	Uncertain significance (Nov 08, 2022)
11-116762603-T-C		not specified	Uncertain significance (Aug 08, 2022)
11-116762606-C-T		not specified	Uncertain significance (Jul 14, 2021)
11-116762712-T-C		not specified	Uncertain significance (Apr 13, 2022)
11-116762769-A-C		not specified	Uncertain significance (Aug 02, 2021)
11-116762786-C-T		not specified	Likely benign (Oct 06, 2022)

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