GABARAP
Basic information
Region (hg38): 17:7240008-7242449
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 GABARAP 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 | 2 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 2 | 0 | 0 |
Variants in GABARAP
This is a list of pathogenic ClinVar variants found in the GABARAP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-7240905-T-G | not specified | Uncertain significance (Sep 27, 2024) | ||
| 17-7242287-C-T | not specified | Uncertain significance (May 05, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GABARAP | protein_coding | protein_coding | ENST00000302386 | 4 | 2757 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.261 | 0.715 | 125706 | 0 | 3 | 125709 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.55 | 31 | 66.6 | 0.465 | 0.00000328 | 766 |
| Missense in Polyphen | 3 | 18.082 | 0.16591 | 216 | ||
| Synonymous | 1.71 | 14 | 24.8 | 0.564 | 0.00000131 | 214 |
| Loss of Function | 1.90 | 2 | 7.68 | 0.260 | 4.67e-7 | 77 |
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) | 0.0000264 | 0.0000264 |
| 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 plays a role in intracellular transport of GABA(A) receptors and its interaction with the cytoskeleton. Involved in apoptosis. Involved in autophagy. 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:15977068}.;
- 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;gamma-aminobutyric acid receptor life cycle pathway;TBC/RABGAPs;Membrane Trafficking;Macroautophagy;Cellular responses to external stimuli;Rab regulation of trafficking
(Consensus)
Recessive Scores
- pRec
- 0.194
Intolerance Scores
- loftool
- 0.382
- rvis_EVS
- 0.1
- rvis_percentile_EVS
- 60.96
Haploinsufficiency Scores
- pHI
- 0.353
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.589
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.965
Mouse Genome Informatics
- Gene name
- Gabarap
- Phenotype
- normal phenotype;
Zebrafish Information Network
- Gene name
- gabarapb
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- autophagosome assembly;microtubule cytoskeleton organization;autophagy of mitochondrion;protein targeting;autophagy;cellular response to nitrogen starvation;chemical synaptic transmission;extrinsic apoptotic signaling pathway via death domain receptors;macroautophagy;autophagosome maturation
- Cellular component
- Golgi membrane;autophagosome membrane;cytoplasm;lysosome;autophagosome;smooth endoplasmic reticulum;cytosol;microtubule;microtubule associated complex;plasma membrane;axoneme;actin cytoskeleton;cytoplasmic vesicle;cell body;perinuclear region of cytoplasm;sperm midpiece
- Molecular function
- protein binding;microtubule binding;ubiquitin protein ligase binding;beta-tubulin binding;GABA receptor binding