U2SURP
protein-codingU2 snRNP associated SURP domain containing, the group of Spliceosomal A complex|RNA binding motif containing
Gene summary
Enables RNA binding activity. Predicted to be involved in RNA processing. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~96.2 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 U2SURP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001080415.2. 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 | 2 | |||
| missense | 62 | 62 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 0 | 0 | 70 | 0 | 1 | 71 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001073884.1 | 28 | MANE Select | |
| Ensembl | ENSP00000418563.1 | 28 | MANE Select | |
| RefSeq | NP_001307148.1 | 28 | Standard | |
| RefSeq | NP_001307149.1 | 16 | Standard |
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
Molecular Function
- RNA binding
- protein binding
Cellular Component
- nucleus
- nucleoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000473835
- Coding exons
- 28
- Length
- 96229
- Individuals with no LoFs
- 123962
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 123964
- p
- 0.00000807
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 4.09 | 245 | 503 | 0.487 | 0.0000261 | 6758 |
| Missense (PolyPhen) | 19 | 136.63 | 0.13906 | 1810 | ||
| Synonymous | -0.473 | 175 | 167 | 1.05 | 0.00000863 | 1818 |
| Loss of Function | 7.13 | 1 | 61.2 | 0.0163 | 0.00000357 | 825 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.00022 | 0.00020 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- -0.91
- RVIS percentile EVS
- 9.9
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |