BMS1
protein-codingBMS1 ribosome biogenesis factor, the group of SSU processome
Gene summary
This gene likely encodes a ribosome assembly protein. A similar protein in yeast functions in 35S-rRNA processing, which includes a series of cleavage steps critical for formation of 40S ribosomes. Related pseudogenes exist on chromosomes 2, 9, 10, 15, 16, and 22.[provided by RefSeq, Mar 2009]
- BMS1L
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~52.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0007145
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0007145
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007145
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Dermatologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BMS1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014753.4. 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 | 3 | 28 | 5 | 36 | ||
| missense | 1 | 179 | 18 | 10 | 208 | |
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 1 | 0 | 190 | 46 | 15 | 252 |
Highest pathogenic variant AF is 0.000009937827
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055568.3 | 22 | MANE Select | |
| Ensembl | ENSP00000363642.4 | 22 | MANE Select | |
| Ensembl | ENSP00000547481.1 | 22 | Standard | |
| Ensembl | ENSP00000547481.1 | 22 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| bms1 | Danio rerio | Structure: intestine Quality: morphology abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ribosome biogenesis in eukaryotes - Homo sapiens (human)
- rRNA processing
- Metabolism of RNA
- rRNA modification in the nucleus and cytosol
- rRNA processing in the nucleus and cytosol
Biological Process
- maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
- rRNA processing
Molecular Function
- RNA binding
- GTPase activity
- ATP binding
- GTP binding
- U3 snoRNA binding
Cellular Component
- nucleus
- nucleoplasm
- nucleolus
- 90S preribosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000374518
- Coding exons
- 22
- Length
- 52137
- Individuals with no LoFs
- 125698
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 50
- Defined
- 125748
- p
- 0.000199
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.260 | 676 | 695 | 0.972 | 0.0000371 | 8498 |
| Missense (PolyPhen) | 184 | 224.15 | 0.82088 | 2827 | ||
| Synonymous | -1.34 | 276 | 249 | 1.11 | 0.0000137 | 2311 |
| Loss of Function | 5.08 | 19 | 62.2 | 0.305 | 0.00000346 | 758 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00026 | 0.00025 | rare |
| Latino/Admixed American | 0.000090 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000095 | 0.000092 | rare |
| European (Non-Finnish) | 0.00025 | 0.00025 | rare |
| South Asian | 0.00037 | 0.00036 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus. {ECO:0000250|UniProtKB:Q08965}.;
- Disease
- DISEASE: Aplasia cutis congenita, non-syndromic (ACC) [MIM:107600]: A disorder characterized by congenital absence of a portion of skin in a localized or widespread area of the body. The lesions are most commonly localized on the scalp, however aplasia cutis congenita can affect any part of the body. {ECO:0000269|PubMed:23785305}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Intolerance Scores
- LoFtool
- 0.645
- RVIS EVS
- 0.1
- RVIS percentile EVS
- 60.76
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.877
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |