GABARAPL2
protein-codingGABA type A receptor associated protein like 2, the group of Autophagy related
Gene summary
Enables phosphatidylethanolamine binding activity and ubiquitin protein ligase binding activity. Involved in autophagosome assembly; negative regulation of proteasomal protein catabolic process; and protein localization to endoplasmic reticulum. Located in Golgi membrane and autophagosome membrane. [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 ~11.5 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 GABARAPL2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_007285.7. 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 | 0 | |||||
| missense | 8 | 8 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 12 | 0 | 0 | 12 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_009216.1 | 4 | MANE Select | |
| Ensembl | ENSP00000037243.2 | 4 | MANE Select | |
| Ensembl | ENSP00000457448.1 | 3 | Standard | |
| Ensembl | ENSP00000457448.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human)
- GABAergic synapse - Homo sapiens (human)
- Autophagy - animal - Homo sapiens (human)
- FoxO signaling pathway - Homo sapiens (human)
- Autophagy - other - Homo sapiens (human)
Biological Process
- autophagosome assembly
- autophagy of mitochondrion
- intra-Golgi vesicle-mediated transport
- autophagy
- cellular response to nitrogen starvation
Molecular Function
- SNARE binding
- protein binding
- microtubule binding
- ubiquitin protein ligase binding
- beta-tubulin binding
Cellular Component
- Golgi membrane
- autophagosome membrane
- cytoplasm
- autophagosome
- Golgi apparatus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000037243
- Coding exons
- 4
- Length
- 11531
- Individuals with no LoFs
- 125670
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 78
- Defined
- 125748
- p
- 0.000310
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.972 | 43 | 65.1 | 0.661 | 0.00000321 | 771 |
| Missense (PolyPhen) | 7 | 17.844 | 0.3923 | 234 | ||
| Synonymous | -0.209 | 26 | 24.7 | 1.05 | 0.00000133 | 204 |
| Loss of Function | 0.442 | 6 | 7.29 | 0.823 | 3.11e-7 | 84 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0045 | 0.0040 | notable |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000062 | 0.000062 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Ubiquitin-like modifier involved in intra-Golgi traffic. Modulates intra-Golgi transport through coupling between NSF activity and SNAREs activation. It first stimulates the ATPase activity of NSF which in turn stimulates the association with GOSR1 (By similarity). Involved in autophagy. Plays a role in mitophagy which contributes to regulate mitochondrial quantity and quality by eliminating the mitochondria to a basal level to fulfill cellular energy requirements and preventing excess ROS production. Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation. {ECO:0000250, ECO:0000269|PubMed:20418806, ECO:0000269|PubMed:23209295}.;
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- LoFtool
- 0.762
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 49.39
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |