SAP30BP
protein-codingSAP30 binding protein
Gene summary
Enables cyclin-dependent protein serine/threonine kinase regulator activity. Involved in regulation of mRNA splicing, via spliceosome. Located in nucleoplasm. Is active in nuclear speck. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~40.8 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 SAP30BP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_013260.8. 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 | 39 | 39 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 46 | 0 | 0 | 46 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_037392.1 | 11 | MANE Select | |
| Ensembl | ENSP00000462116.1 | 11 | MANE Select | |
| RefSeq | NP_001288768.1 | 10 | Standard | |
| RefSeq | NP_001288784.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- NoRC negatively regulates rRNA expression
- Negative epigenetic regulation of rRNA expression
- Epigenetic regulation of gene expression
- Gene expression (Transcription)
Biological Process
- regulation of transcription, DNA-templated
- apoptotic process
- positive regulation of cell death
Molecular Function
- protein binding
Cellular Component
- nucleus
- nucleoplasm
- intermediate filament cytoskeleton
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000584667
- Coding exons
- 11
- Length
- 40947
- Individuals with no LoFs
- 125587
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 161
- Defined
- 125748
- p
- 0.000640
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.75 | 114 | 180 | 0.634 | 0.00000992 | 2013 |
| Missense (PolyPhen) | 36 | 70.315 | 0.51198 | 809 | ||
| Synonymous | 0.0159 | 69 | 69.2 | 0.998 | 0.00000428 | 568 |
| Loss of Function | 2.28 | 10 | 21.4 | 0.468 | 0.00000117 | 241 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.0049 | 0.0050 | notable |
| European (Non-Finnish) | 0.00034 | 0.00033 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0.0011 | 0.0011 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Induces cell death. May act as a transcriptional corepressor of a gene related to cell survival. May be involved in the regulation of beta-2-microglobulin genes. {ECO:0000250|UniProtKB:Q02614, ECO:0000269|PubMed:15496587}.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- LoFtool
- 0.461
- RVIS EVS
- -0.12
- RVIS percentile EVS
- 44.89
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.985