GPATCH3
protein-codingG-patch domain containing 3, the group of G-patch domain containing
Gene summary
Predicted to enable nucleic acid binding activity. Involved in negative regulation of RIG-I signaling pathway; negative regulation of type I interferon production; and positive regulation of DNA-templated transcription. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
- GPATC3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~10.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0020366
Submitter: G2P
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GPATCH3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022078.3. 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 | 1 | 3 | 4 | |||
| missense | 87 | 5 | 92 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 88 | 8 | 0 | 96 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071361.2 | 7 | MANE Select | |
| Ensembl | ENSP00000354645.5 | 7 | MANE Select | |
| Ensembl | ENSP00000398563.1 | 3 | Standard | |
| Ensembl | ENSP00000399036.1 | 3 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| gpatch3 | Danio rerio | Structure: iridophore Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of type I interferon production
- negative regulation of RIG-I signaling pathway
- positive regulation of transcription, DNA-templated
Molecular Function
- nucleic acid binding
- protein binding
Cellular Component
- nucleus
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000361720
- Coding exons
- 7
- Length
- 9979
- Individuals with no LoFs
- 125532
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 216
- Defined
- 125748
- p
- 0.000859
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.226 | 327 | 316 | 1.04 | 0.0000183 | 3379 |
| Missense (PolyPhen) | 119 | 115.44 | 1.0308 | 1191 | ||
| Synonymous | -0.213 | 127 | 124 | 1.02 | 0.00000626 | 1099 |
| Loss of Function | 0.534 | 22 | 24.9 | 0.885 | 0.00000125 | 267 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00035 | 0.00035 | rare |
| Ashkenazi Jewish | 0.00060 | 0.00060 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00092 | 0.00083 | rare |
| European (Non-Finnish) | 0.0013 | 0.0013 | notable |
| South Asian | 0.00082 | 0.00082 | rare |
| Other | 0.00098 | 0.00098 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in transcriptional regulation. It is able to activate transcription from the CXCR4 promoter and therefore it might control neural crest cell migration involved in ocular and craniofacial development (PubMed:28397860). Is a negative regulator of immune antiviral response, acting via down-regulation of RIG-I-like receptors signaling and inhibition of type I interferon production. The control mechanism involves interaction with mitochondrial MAVS and inhibition of MAVS assembly with downstream proteins implicated in antiviral response, such as TBK1 and TRAF6 (PubMed:28414768). {ECO:0000269|PubMed:28397860, ECO:0000269|PubMed:28414768}.;
Intolerance Scores
- LoFtool
- 0.924
- RVIS EVS
- -0.55
- RVIS percentile EVS
- 19.8
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.931
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |