SCAI
protein-codingsuppressor of cancer cell invasion
Gene summary
This gene encodes a regulator of cell migration. The encoded protein appears to function in the RhoA (ras homolog gene family, member A)-Dia1 (diaphanous homolog 1) signal transduction pathway. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]
- C9orf126
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~200.9 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 SCAI variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001144877.3. 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 | 2 | 2 | ||||
| missense | 54 | 54 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 57 | 2 | 0 | 59 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001138349.1 | 18 | MANE Select | |
| Ensembl | ENSP00000336756.6 | 18 | MANE Select | |
| RefSeq | NP_775961.2 | 19 | Standard | |
| Ensembl | ENSP00000362650.4 | 19 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Signal Transduction
- RHO GTPases Activate Formins
- RHO GTPase Effectors
- Signaling by Rho GTPases
- RhoA signaling pathway
Biological Process
- transcription, DNA-templated
- negative regulation of cell migration
- negative regulation of Rho protein signal transduction
- negative regulation of nucleic acid-templated transcription
Molecular Function
- transcription corepressor activity
- protein binding
Cellular Component
- nucleus
- nucleoplasm
- cytoplasm
- integral component of membrane
- nuclear membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000373549
- Coding exons
- 19
- Length
- 200899
- Individuals with no LoFs
- 124782
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 124787
- p
- 0.0000200
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.01 | 178 | 332 | 0.535 | 0.0000176 | 4104 |
| Missense (PolyPhen) | 23 | 82.655 | 0.27826 | 1004 | ||
| Synonymous | 0.456 | 112 | 118 | 0.947 | 0.00000605 | 1178 |
| Loss of Function | 5.39 | 5 | 43.2 | 0.116 | 0.00000255 | 487 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000059 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Tumor suppressor which functions to suppress MRTFA- induced SRF transcriptional activity. May function in the RHOA- DIAPH1 signal transduction pathway and regulate cell migration through transcriptional regulation of ITGB1. {ECO:0000269|PubMed:19350017}.;
Recessive Scores
- pRec
- 0.0917
Intolerance Scores
- LoFtool
- 0.321
- RVIS EVS
- -0.49
- RVIS percentile EVS
- 22.36
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.231
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |