GLIPR2
protein-codingGLI pathogenesis related 2, the group of CAP superfamily
Gene summary
Enables protein homodimerization activity. Involved in positive regulation of ERK1 and ERK2 cascade; positive regulation of epithelial cell migration; and positive regulation of epithelial to mesenchymal transition. Located in Golgi membrane. Biomarker of pancreatic ductal adenocarcinoma. [provided by Alliance of Genome Resources, Jul 2025]
- C9orf19
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~27.4 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 GLIPR2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022343.4. 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 | 1 | 1 | 2 | |||
| missense | 28 | 28 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 30 | 1 | 1 | 32 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071738.1 | 5 | MANE Select | |
| Ensembl | ENSP00000367196.4 | 5 | MANE Select | |
| RefSeq | NP_001273939.1 | 4 | Standard | |
| RefSeq | NP_001273940.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- positive regulation of epithelial cell migration
- positive regulation of epithelial to mesenchymal transition
- positive regulation of ERK1 and ERK2 cascade
Molecular Function
- protein homodimerization activity
Cellular Component
- Golgi membrane
- extracellular space
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000377960
- Coding exons
- 5
- Length
- 27179
- Individuals with no LoFs
- 125543
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 205
- Defined
- 125748
- p
- 0.000815
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.307 | 87 | 95.4 | 0.912 | 0.00000591 | 1018 |
| Missense (PolyPhen) | 26 | 31.284 | 0.83108 | 328 | ||
| Synonymous | -0.0665 | 42 | 41.5 | 1.01 | 0.00000300 | 272 |
| Loss of Function | 0.344 | 7 | 8.05 | 0.869 | 3.41e-7 | 104 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.0071 | 0.0070 | notable |
| European (Non-Finnish) | 0.00034 | 0.00033 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.00099 | 0.00098 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.120
Intolerance Scores
- LoFtool
- 0.720
- RVIS EVS
- -0.38
- RVIS percentile EVS
- 27.42
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.223
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |