SRP9
protein-codingsignal recognition particle 9, the group of Signal recognition particle
Gene summary
Predicted to enable RNA binding activity and signal recognition particle binding activity. Predicted to be involved in SRP-dependent cotranslational protein targeting to membrane. Predicted to be located in cytosol. Predicted to be part of signal recognition particle, endoplasmic reticulum targeting. [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 ~12.7 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 SRP9 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003133.6. 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 | 5 | 1 | 6 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 5 | 1 | 0 | 6 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003124.1 | 3 | MANE Select | |
| Ensembl | ENSP00000305230.7 | 3 | MANE Select | |
| RefSeq | NP_001123912.1 | 3 | Standard | |
| Ensembl | ENSP00000355803.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Protein export - Homo sapiens (human)
- SRP-dependent cotranslational protein targeting to membrane
- Translation
- Metabolism of proteins
- IL3-mediated signaling events
Biological Process
- SRP-dependent cotranslational protein targeting to membrane
- SRP-dependent cotranslational protein targeting to membrane, translocation
- negative regulation of translational elongation
Molecular Function
- RNA binding
- signal recognition particle binding
- protein binding
- 7S RNA binding
Cellular Component
- signal recognition particle receptor complex
- signal recognition particle, endoplasmic reticulum targeting
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000304786
- Coding exons
- 3
- Length
- 12638
- Individuals with no LoFs
- 125585
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125588
- p
- 0.0000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.13 | 26 | 47.9 | 0.543 | 0.00000247 | 570 |
| Missense (PolyPhen) | 4 | 11.786 | 0.3394 | 164 | ||
| Synonymous | 0.0839 | 15 | 15.4 | 0.973 | 6.72e-7 | 143 |
| Loss of Function | 1.72 | 1 | 5.24 | 0.191 | 2.97e-7 | 58 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Signal-recognition-particle assembly has a crucial role in targeting secretory proteins to the rough endoplasmic reticulum membrane. SRP9 together with SRP14 and the Alu portion of the SRP RNA, constitutes the elongation arrest domain of SRP. The complex of SRP9 and SRP14 is required for SRP RNA binding.;
Recessive Scores
- pRec
- 0.164
Intolerance Scores
- LoFtool
- 0.289
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 49.39
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.982
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |