BUD31

protein-coding

BUD31 homolog, the group of Spliceosomal B complex|Spliceosomal Bact complex|Spliceosomal P complex|NTC associated proteins|Spliceosomal C complex

Gene summary

Enables nuclear receptor binding activity and transcription coactivator activity. Involved in mRNA splicing, via spliceosome. Located in chromatin and nucleoplasm. Part of U2-type catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

MANE transcript

NM_003910.4

Inheritance

—

ClinVar variants

U:17

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr7:99,408,641-99,419,616

External References & Databases

Ensembl (ENSG00000106245)

Transcript & Mutation Effects

hg38 • Region Span ~11.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BUD31 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003910.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			15 clinvar			15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	17	0	0	17

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 79 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003910.4	RefSeq	NP_003901.2	4	MANE Select
ENST00000222969.10	Ensembl	ENSP00000222969.5	4	MANE Select
NM_001370407.1	RefSeq	NP_001357336.1	4	Standard
NM_001370410.1	RefSeq	NP_001357339.1	4	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
bud31	Danio rerio	Structure: head Quality: flat abnormal

Gene / Model

Organism

Observed Phenotype

bud31

Danio rerio

Structure: head

Quality: flat

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)
Metabolism of RNA
mRNA Splicing - Major Pathway
mRNA Splicing
Processing of Capped Intron-Containing Pre-mRNA

Biological Process

mRNA splicing, via spliceosome
positive regulation of nucleic acid-templated transcription
positive regulation of androgen receptor activity

Molecular Function

protein binding
nuclear receptor transcription coactivator activity
nuclear hormone receptor binding

Cellular Component

nuclear chromatin
nucleus
nucleoplasm
spliceosomal complex
U2-type catalytic step 2 spliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000403633
Coding exons: 4
Length: 10976
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125748
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.34	54	89.7	0.602	0.00000571	948
Missense (PolyPhen)		18	27.772	0.64815		331
Synonymous	0.439	28	31.1	0.900	0.00000180	250
Loss of Function	1.81	2	7.26	0.275	3.03e-7	100

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the pre-mRNA splicing process (PubMed:28502770, PubMed:28076346). May play a role as regulator of AR transcriptional activity; may increase AR transcriptional activity (PubMed:25091737). {ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770, ECO:0000305|PubMed:25091737}.;

Recessive Scores

pRec: 0.124

Intolerance Scores

LoFtool: 0.283
RVIS EVS: -0.03
RVIS percentile EVS: 51.04

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.896

Gene Damage Prediction

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