GABARAPL2
GABA type A receptor associated protein like 2, the group of Autophagy related
Basic information
Region (hg38): 16:75566375-75577881
Links
Phenotypes
GenCC
Source:
No genCC data.
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 GABARAPL2 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 GABARAPL2
This is a list of pathogenic ClinVar variants found in the GABARAPL2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-75566503-A-G | not specified | Uncertain significance (Oct 20, 2024) | ||
| 16-75566505-G-A | not specified | Uncertain significance (Apr 15, 2024) | ||
| 16-75568068-T-C | not specified | Uncertain significance (Feb 16, 2023) | ||
| 16-75577329-T-C | not specified | Uncertain significance (Sep 10, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GABARAPL2 | protein_coding | protein_coding | ENST00000037243 | 4 | 11531 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000228 | 0.529 | 125670 | 0 | 78 | 125748 | 0.000310 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.972 | 43 | 65.1 | 0.661 | 0.00000321 | 771 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00464 | 0.00412 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000617 | 0.0000615 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000334 | 0.0000327 |
| Other | 0.000171 | 0.000163 |
dbNSFP
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}.;
- 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;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Macroautophagy;Cellular responses to external stimuli;Rab regulation of trafficking
(Consensus)
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.762
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.39
Haploinsufficiency Scores
- pHI
- 0.368
- hipred
- Y
- hipred_score
- 0.813
- ghis
- 0.619
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Gabarapl2
- Phenotype
- homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- autophagosome assembly;autophagy of mitochondrion;intra-Golgi vesicle-mediated transport;autophagy;cellular response to nitrogen starvation;protein transport;macroautophagy;positive regulation of ATPase activity;autophagosome maturation;negative regulation of proteasomal protein catabolic process
- Cellular component
- Golgi membrane;autophagosome membrane;cytoplasm;autophagosome;Golgi apparatus;cytosol;cytoplasmic vesicle
- Molecular function
- SNARE binding;protein binding;microtubule binding;ubiquitin protein ligase binding;beta-tubulin binding;GABA receptor binding;ATPase binding