GABARAPL1
Basic information
Region (hg38): 12:10212458-10223128
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GABARAPL1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 0 |
Variants in GABARAPL1
This is a list of pathogenic ClinVar variants found in the GABARAPL1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-10213161-T-C | not specified | Uncertain significance (Apr 01, 2024) | ||
| 12-10213215-T-A | not specified | Uncertain significance (Jul 07, 2024) | ||
| 12-10218096-C-T | not specified | Uncertain significance (Jan 28, 2025) | ||
| 12-10220541-A-G | not specified | Uncertain significance (Dec 27, 2022) | ||
| 12-10220542-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
| 12-10221806-A-G | not specified | Uncertain significance (Mar 08, 2025) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GABARAPL1 | protein_coding | protein_coding | ENST00000266458 | 4 | 10671 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.835 | 0.162 | 125746 | 0 | 1 | 125747 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.19 | 36 | 62.5 | 0.576 | 0.00000291 | 769 |
| Missense in Polyphen | 13 | 20.396 | 0.63739 | 258 | ||
| Synonymous | -0.425 | 26 | 23.4 | 1.11 | 0.00000111 | 201 |
| Loss of Function | 2.26 | 0 | 5.94 | 0.00 | 2.56e-7 | 80 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ubiquitin-like modifier that increases cell-surface expression of kappa-type opioid receptor through facilitating anterograde intracellular trafficking of the receptor. Involved in formation of autophagosomal vacuoles. 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:0000269|PubMed:16431922, ECO:0000269|PubMed:20404487}.;
- Pathway
- 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);Mitophagy - animal - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Senescence and Autophagy in Cancer;Macroautophagy;Cellular responses to external stimuli
(Consensus)
Recessive Scores
- pRec
- 0.142
Intolerance Scores
- loftool
- 0.299
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.590
- ghis
- 0.574
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Gabarapl1
- Phenotype
Gene ontology
- Biological process
- autophagosome assembly;autophagy of mitochondrion;cellular response to nitrogen starvation;macroautophagy;autophagosome maturation
- Cellular component
- autophagosome membrane;mitochondrion;autophagosome;endoplasmic reticulum;Golgi apparatus;cytosol;microtubule;cytoplasmic vesicle membrane;dendrite membrane;dendrite cytoplasm;cell body
- Molecular function
- protein binding;Tat protein binding;ubiquitin protein ligase binding;beta-tubulin binding;GABA receptor binding