GSG1
protein-codinggerm cell associated 1
Gene summary
Predicted to enable RNA polymerase binding activity. Predicted to be located in endoplasmic reticulum. Predicted to be active in plasma membrane. [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 ~20.2 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 GSG1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001080555.4. 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 | 7 | 9 | |||
| missense | 53 | 6 | 59 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 55 | 13 | 0 | 68 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001074024.1 | 7 | MANE Select | |
| Ensembl | ENSP00000498528.1 | 7 | MANE Select | |
| RefSeq | NP_001074023.1 | 7 | Standard | |
| RefSeq | NP_001193771.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- protein binding
- RNA polymerase binding
Cellular Component
- endoplasmic reticulum membrane
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000432710
- Coding exons
- 6
- Length
- 20126
- Individuals with no LoFs
- 124772
- Homozygous LoFs
- 4
- Heterozygous LoFs
- 968
- Defined
- 125744
- p
- 0.00387
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.224 | 184 | 193 | 0.955 | 0.0000105 | 2206 |
| Missense (PolyPhen) | 53 | 58.342 | 0.90844 | 741 | ||
| Synonymous | 0.351 | 76 | 80.0 | 0.950 | 0.00000460 | 677 |
| Loss of Function | 1.77 | 7 | 14.2 | 0.494 | 6.90e-7 | 148 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00086 | 0.00086 | rare |
| Latino/Admixed American | 0.0019 | 0.0019 | notable |
| Ashkenazi Jewish | 0.0015 | 0.0015 | notable |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.0031 | 0.0031 | notable |
| European (Non-Finnish) | 0.0063 | 0.0063 | notable |
| South Asian | 0.0022 | 0.0022 | notable |
| Other | 0.0049 | 0.0049 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May cause the redistribution of PAPOLB from the cytosol to the endoplasmic reticulum. {ECO:0000250}.;
Intolerance Scores
- LoFtool
- 0.920
- RVIS EVS
- 1.06
- RVIS percentile EVS
- 91.58
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.170
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |