GPSM3
protein-codingG protein signaling modulator 3
Gene summary
Predicted to enable GTPase regulator activity. Predicted to be involved in positive regulation of inflammatory response. Predicted to act upstream of or within positive regulation of cytokine production involved in inflammatory response and positive regulation of leukocyte chemotaxis. Predicted to be located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]
- C6orf9
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.8 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 GPSM3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001276501.2. 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 | 18 | 2 | 1 | 21 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 20 | 2 | 2 | 24 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001263430.1 | 4 | MANE Select | |
| Ensembl | ENSP00000364180.3 | 4 | MANE Select | |
| RefSeq | NP_071390.1 | 4 | Standard | |
| Ensembl | ENSP00000364183.3 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Signaling by GPCR
- Signal Transduction
- G alpha (i) signalling events
- GPCR downstream signalling
Biological Process
- positive regulation of leukocyte chemotaxis
- biological_process
- positive regulation of inflammatory response
- regulation of catalytic activity
- positive regulation of cytokine production involved in inflammatory response
Molecular Function
- molecular_function
- protein binding
- GTPase regulator activity
Cellular Component
- cellular_component
- cytoplasm
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000375040
- Coding exons
- 4
- Length
- 4758
- Individuals with no LoFs
- 125548
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 14
- Defined
- 125562
- p
- 0.0000558
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.865 | 67 | 90.1 | 0.744 | 0.00000539 | 986 |
| Missense (PolyPhen) | 23 | 38.276 | 0.60089 | 399 | ||
| Synonymous | 1.98 | 19 | 33.6 | 0.565 | 0.00000160 | 346 |
| Loss of Function | 1.97 | 2 | 8.00 | 0.250 | 4.17e-7 | 84 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000072 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000095 | 0.000088 | rare |
| South Asian | 0.000069 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Interacts with subunit of G(i) alpha proteins and regulates the activation of G(i) alpha proteins. {ECO:0000269|PubMed:14656218, ECO:0000269|PubMed:15096500}.;
Intolerance Scores
- LoFtool
- 0.492
- RVIS EVS
- 0.19
- RVIS percentile EVS
- 66.57
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.803
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |