GIT1
protein-codingGIT ArfGAP 1, the group of Ankyrin repeat domain containing|ArfGAPs
Gene summary
Enables gamma-tubulin binding activity. Involved in positive regulation of microtubule nucleation and regulation of cytokinesis. Located in cytosol; focal adhesion; and microtubule cytoskeleton. Implicated in attention deficit hyperactivity disorder. Biomarker of Huntington's disease. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~20.6 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 GIT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014030.4. 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 | 13 | 2 | 16 | ||
| missense | 79 | 2 | 81 | |||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 1 | 2 | 3 | |||
| splice donor/acceptor (+/-2bp) | 1 | 12 | 13 | |||
| Total | 2 | 0 | 95 | 15 | 2 | 114 |
Highest pathogenic variant AF is 6.890526e-7
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_054749.2 | 20 | MANE Select | |
| Ensembl | ENSP00000225394.3 | 20 | MANE Select | |
| RefSeq | NP_001078923.1 | 21 | Standard | |
| Ensembl | ENSP00000334125.7 | 5 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| git1 | Danio rerio | Structure: central artery Quality: decreased length abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Endocytosis - Homo sapiens (human)
- Regulation of actin cytoskeleton - Homo sapiens (human)
- Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human)
- Regulation of Actin Cytoskeleton
- Developmental Biology
Biological Process
- regulation of G protein-coupled receptor signaling pathway
- regulation of cytokinesis
- positive regulation of GTPase activity
- ephrin receptor signaling pathway
- presynaptic modulation of chemical synaptic transmission
Molecular Function
- GTPase activator activity
- protein binding
- protein-containing complex binding
- metal ion binding
Cellular Component
- cytosol
- focal adhesion
- membrane
- calyx of Held
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000394869
- Coding exons
- 21
- Length
- 20586
- Individuals with no LoFs
- 125734
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 125739
- p
- 0.0000199
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.06 | 294 | 483 | 0.608 | 0.0000316 | 4974 |
| Missense (PolyPhen) | 81 | 179.83 | 0.45042 | 1848 | ||
| Synonymous | 0.658 | 193 | 205 | 0.942 | 0.0000141 | 1555 |
| Loss of Function | 5.41 | 4 | 41.7 | 0.0960 | 0.00000210 | 463 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000094 | 0.000092 | rare |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0.000035 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: GTPase-activating protein for the ADP ribosylation factor family. May serve as a scaffold to bring together molecules to form signaling modules controlling vesicle trafficking, adhesion and cytoskeletal organization. Increases the speed of cell migration, as well as the size and rate of formation of protrusions, possibly by targeting PAK1 to adhesions and the leading edge of lamellipodia. Sequesters inactive non-tyrosine- phosphorylated paxillin in cytoplasmic complexes. Involved in the regulation of cytokinesis; the function may involve ENTR1 and PTPN13 (By similarity). {ECO:0000250|UniProtKB:Q68FF6, ECO:0000269|PubMed:11896197}.;
Recessive Scores
- pRec
- 0.176
Intolerance Scores
- LoFtool
- 0.355
- RVIS EVS
- -1.4
- RVIS percentile EVS
- 4.19
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.843
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |