SNRNP48
protein-codingsmall nuclear ribonucleoprotein U11/U12 subunit 48, the group of U11/U12 di-snRNP|U11 small nuclear ribonucleoprotein
Gene summary
Predicted to enable zinc ion binding activity. Predicted to be involved in spliceosome conformational change to release U4 (or U4atac) and U1 (or U11). Located in nucleoplasm. Part of U12-type spliceosomal complex. [provided by Alliance of Genome Resources, Jun 2026]
- C6orf151
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.8 kbGenCC 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 SNRNP48 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152551.4. 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 | 1 | ||||
| missense | 49 | 49 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 50 | 1 | 0 | 51 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689764.3 | 9 | MANE Select | |
| Ensembl | ENSP00000339834.4 | 9 | MANE Select | |
| Ensembl | ENSP00000489245.1 | 6 | Standard | |
| Ensembl | ENSP00000535037.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of RNA
- mRNA Splicing - Minor Pathway
- mRNA Splicing
- Processing of Capped Intron-Containing Pre-mRNA
Biological Process
- mRNA splicing, via spliceosome
- RNA splicing
Molecular Function
- metal ion binding
Cellular Component
- nucleoplasm
- U12-type spliceosomal complex
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000342415
- Coding exons
- 9
- Length
- 21769
- Individuals with no LoFs
- 125712
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 22
- Defined
- 125734
- p
- 0.0000875
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.37 | 114 | 163 | 0.697 | 0.00000840 | 2209 |
| Missense (PolyPhen) | 17 | 38.279 | 0.44411 | 526 | ||
| Synonymous | 0.668 | 50 | 56.4 | 0.887 | 0.00000273 | 583 |
| Loss of Function | 0.987 | 15 | 19.7 | 0.760 | 0.00000123 | 251 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00010 | 0.000097 | rare |
| South Asian | 0.00015 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Likely involved in U12-type 5' splice site recognition. {ECO:0000269|PubMed:19217400}.;
Intolerance Scores
- LoFtool
- 0.883
- RVIS EVS
- -0.25
- RVIS percentile EVS
- 35.99
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.875
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |