SSX5
protein-codingSSX family member 5, the group of SSX family
Gene summary
The product of this gene belongs to the family of highly homologous synovial sarcoma X (SSX) breakpoint proteins. These proteins may function as transcriptional repressors. They are also capable of eliciting spontaneous humoral and cellular immune responses in cancer patients, and are potentially useful targets in cancer vaccine-based immunotherapy. While some of the related SSX genes are involved in t(X;18)(p11.2;q11.2) translocations that are characteristically found in all synovial sarcomas, this gene does not appear to be involved in such translocations. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~10.6 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 SSX5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_175723.2. 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 | ||||
| missense | 39 | 9 | 48 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 41 | 10 | 0 | 51 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_783729.1 | 6 | MANE Select | |
| Ensembl | ENSP00000290558.1 | 6 | MANE Select | |
| RefSeq | NP_066295.3 | 7 | Standard | |
| Ensembl | ENSP00000312415.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of transcription, DNA-templated
Molecular Function
- nucleic acid binding
- protein binding
Cellular Component
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000311798
- Coding exons
- 7
- Length
- 10544
- Individuals with no LoFs
- 125636
- Homozygous LoFs
- 32
- Heterozygous LoFs
- 67
- Defined
- 125735
- p
- 0.000394
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.31 | 134 | 97.7 | 1.37 | 0.00000804 | 1521 |
| Missense (PolyPhen) | 24 | 25.062 | 0.95762 | 491 | ||
| Synonymous | -3.20 | 59 | 35.0 | 1.69 | 0.00000305 | 402 |
| Loss of Function | -0.675 | 11 | 8.84 | 1.24 | 5.57e-7 | 164 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0068 | 0.0053 | notable |
| Latino/Admixed American | 0.00012 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000099 | 0.000070 | rare |
| South Asian | 0.000063 | 0.000033 | rare |
| Other | 0.00025 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Could act as a modulator of transcription.;
Recessive Scores
- pRec
- 0.0768
Intolerance Scores
- LoFtool
- 0.950
- RVIS EVS
- 1.51
- RVIS percentile EVS
- 95.41
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |