SRSF12
protein-codingserine and arginine rich splicing factor 12, the group of RNA binding motif containing|Serine and arginine rich splicing factors
Gene summary
Enables RNA binding activity. Involved in mRNA 5'-splice site recognition and regulation of alternative mRNA splicing, via spliceosome. Predicted to be located in nucleoplasm. Predicted to be active in nuclear speck. [provided by Alliance of Genome Resources, Jul 2025]
- SFRS13B
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~24.1 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 SRSF12 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_080743.5. 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 | 0 | |||||
| missense | 32 | 32 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 32 | 0 | 0 | 32 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_542781.3 | 5 | MANE Select | |
| Ensembl | ENSP00000414302.2 | 5 | MANE Select | |
| RefSeq | NP_001363825.1 | 2 | Standard | |
| RefSeq | NP_001363826.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- spliceosomal tri-snRNP complex assembly
- regulation of alternative mRNA splicing, via spliceosome
- mRNA 5'-splice site recognition
- mRNA cis splicing, via spliceosome
- negative regulation of mRNA splicing, via spliceosome
Molecular Function
- RNA binding
- RS domain binding
- unfolded protein binding
Cellular Component
- nucleoplasm
- nuclear speck
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000452027
- Coding exons
- 5
- Length
- 22123
- Individuals with no LoFs
- 124654
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 10
- Defined
- 124664
- p
- 0.0000401
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.11 | 115 | 154 | 0.749 | 0.00000933 | 1652 |
| Missense (PolyPhen) | 21 | 27.895 | 0.75283 | 259 | ||
| Synonymous | 1.14 | 39 | 49.2 | 0.793 | 0.00000234 | 527 |
| Loss of Function | 2.33 | 5 | 14.6 | 0.343 | 9.63e-7 | 163 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000059 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000036 | 0.000035 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00017 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Splicing factor that seems to antagonize SR proteins in pre-mRNA splicing regulation. {ECO:0000269|PubMed:11684676}.;
Intolerance Scores
- RVIS EVS
- 0.33
- RVIS percentile EVS
- 73.11
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- 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 |