GTPBP2

protein-coding

GTP 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

NM_019096.5

Inheritance

AR

ClinVar variants

P:13U:75B:70

Top phenotype

Jaberi-Elahi syndrome

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr6:43,605,316-43,629,264

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~23.9 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Jaberi-Elahi syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0060711

Submitter: Labcorp Genetics (formerly Invitae)

Jaberi-Elahi syndromeDEFINITIVE

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).

Jaberi-Elahi syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0060711

Submitter: Genomics England PanelApp

Jaberi-Elahi syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0060711

Submitter: G2P

Jaberi-Elahi syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0060711

Submitter: Ambry Genetics

Jaberi-Elahi syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0060711

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Jaberi-Elahi syndromeAR

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

Refs: 26675814; 29449720; 38118446Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GTPBP2 variants in ClinVar

7 Conditions Cataloged
not providedTotal: 128
Inborn genetic diseasesTotal: 44
Jaberi-Elahi syndromeTotal: 18
not specifiedTotal: 6
GTPBP2-related disorderTotal: 5
Intellectual disabilityTotal: 1
See casesTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
61
clinvar
5
clinvar
70
missense
67
clinvar
3
clinvar
1
clinvar
71
nonsense
6
clinvar
1
clinvar
7
start loss
0
frameshift
2
clinvar
3
clinvar
5
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
3
clinvar
5
Total9475646158

Highest pathogenic variant AF is 0.0000037177947

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_019096.5RefSeqNP_061969.312MANE Select
ENST00000307126.10EnsemblENSP00000303997.512MANE Select
NM_001286216.2RefSeqNP_001273145.110Standard
ENST00000307114.11EnsemblENSP00000304893.710Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.431823670.4960.00002303869
Missense (PolyPhen)49152.80.320681598
Synonymous-0.09641511501.010.000008771290
Loss of Function3.93730.40.2310.00000200304

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American00.0absent
Ashkenazi Jewish0.000100.000099rare
East Asian00.0absent
Finnish0.0000920.000092rare
European (Non-Finnish)0.0000620.000062rare
South Asian0.000160.00016rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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