GTPBP2
protein-codingGTP binding protein 2
Gene summary
GTP-binding proteins, or G proteins, constitute a superfamily capable of binding GTP or GDP. G proteins are activated by binding GTP and are inactivated by hydrolyzing GTP to GDP. This general mechanism enables G proteins to perform a wide range of biologic activities.[supplied by OMIM, Jan 2003]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~23.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0060711
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0060711
Submitter: ClinGen
The *GTPBP2* (guanosine triphosphate binding protein 2) gene is located on chromosome 6 at 6p21 and encodes a member of the GTP-binding superfamily. This gene was first reported in connection with Jaberi-Elahi syndrome (JABELS) in 2016 (Jaberi et a., PMID: 26675814). This disorder is characterized by developmental, neurological (epilepsy, contractures and/or hypotonia), craniofacial (microcephaly and/or facial dysmorphism), skeletal (scoliosis or kyphoscoliosis), ectodermal (thin, sparse hair, eyebrows and/or abnormal dentition), and ocular features (retinal degeneration, cataract, and/or visual impairment). More recently, this condition has also been described as Gtpbp1/2-related ectodermal neurodevelopmental (GREND) syndrome) (Salpietro et al., 2024, PMID:38118446). Disease severity is highly variable. Some patients have social interaction and learn to walk but have an ataxic gait and abnormal movements, while others do not achieve any motor control, are non-ambulatory and nonverbal. Only the first reported family was found to have iron accumulation in the brain, but these individuals were clinically examined later in adulthood, while more recent reports were examined in childhood. It is possible that the iron accumulation brain phenotype is a later onset manifestation of disease. The mode of inheritance is autosomal recessive; all but two of the reported affected families to date have been consanguineous. The mechanism of disease appears to be loss of function, as most variants identified are truncations, frameshifts, or splice variants, though 5 missense variants have also been reported. At least eight unique variants (5 nonsense, 2 splice-site, 1 missense) that have been reported in eight probands from five publications (PMIDs: 26675814, 28454995, 29449720, 30790272, 38852771) are included in this curation. More evidence is available in the literature, but the maximum score for genetic evidence (12 pts) has been reached. This gene-disease relationship is also supported by experimental evidence, including a mouse model with a splice donor variant in intron 6 of gtpbp2 which recapitulates the cerebellar, retinal, and gait abnormalities found in humans (Ishimura et al., 2014, PMID: 25061210). Crossing mice with this variant to a different strain with gtpbp2 intact rescues the disease phenotypes. In addition, expression studies of human postmortem brain tissue show that *GTPBP2* is highly expressed in the brain regions disrupted in JABELS/GRENDS patients (Salpietro et al., 2024, PMID: 38118446). In summary, there is definitive evidence supporting the relationship between *GTPBP2* and autosomal recessive JABELS/GREND syndrome. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Syndromic Disorders GCEP on the meeting date August 16th, 2024 (SOP Version 10).
Inheritance Pattern: AR
Disease ID:MONDO:0060711
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0060711
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0060711
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0060711
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Dermatologic; Musculoskeletal; Neurologic; Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GTPBP2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_019096.5. 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 | 4 | 61 | 5 | 70 | ||
| missense | 67 | 3 | 1 | 71 | ||
| nonsense | 6 | 1 | 7 | |||
| start loss | 0 | |||||
| frameshift | 2 | 3 | 5 | |||
| splice donor/acceptor (+/-2bp) | 1 | 1 | 3 | 5 | ||
| Total | 9 | 4 | 75 | 64 | 6 | 158 |
Highest pathogenic variant AF is 0.0000037177947
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_061969.3 | 12 | MANE Select | |
| Ensembl | ENSP00000303997.5 | 12 | MANE Select | |
| RefSeq | NP_001273145.1 | 10 | Standard | |
| Ensembl | ENSP00000304893.7 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Platelet degranulation
- Response to elevated platelet cytosolic Ca2+
- Platelet activation, signaling and aggregation
- Hemostasis
Biological Process
- platelet degranulation
- translational elongation
- biological_process
Molecular Function
- translation elongation factor activity
- GTPase activity
- protein binding
- GTP binding
Cellular Component
- extracellular region
- platelet alpha granule lumen
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000307126
- Coding exons
- 12
- Length
- 23847
- Individuals with no LoFs
- 125732
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 16
- Defined
- 125748
- p
- 0.0000636
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.43 | 182 | 367 | 0.496 | 0.0000230 | 3869 |
| Missense (PolyPhen) | 49 | 152.8 | 0.32068 | 1598 | ||
| Synonymous | -0.0964 | 151 | 150 | 1.01 | 0.00000877 | 1290 |
| Loss of Function | 3.93 | 7 | 30.4 | 0.231 | 0.00000200 | 304 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.000062 | 0.000062 | rare |
| South Asian | 0.00016 | 0.00016 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.135
Intolerance Scores
- LoFtool
- 0.516
- RVIS EVS
- -0.43
- RVIS percentile EVS
- 25.37
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.860
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |