SH3GLB1
SH3 domain containing GRB2 like, endophilin B1, the group of N-BAR domain containing|Protein phosphatase 1 regulatory subunits
Basic information
Region (hg38): 1:86704570-86748184
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (39 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3GLB1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016009.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 34 | 34 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 34 | 0 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SH3GLB1 | protein_coding | protein_coding | ENST00000482504 | 11 | 43609 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.994 | 0.00593 | 125737 | 0 | 5 | 125742 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.63 | 130 | 194 | 0.671 | 0.00000914 | 2531 |
| Missense in Polyphen | 46 | 84.375 | 0.54518 | 1098 | ||
| Synonymous | 1.01 | 56 | 66.5 | 0.843 | 0.00000312 | 704 |
| Loss of Function | 3.90 | 1 | 19.7 | 0.0509 | 8.27e-7 | 278 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000647 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000604 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000265 | 0.0000264 |
| Middle Eastern | 0.0000604 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be required for normal outer mitochondrial membrane dynamics (PubMed:15452144). Required for coatomer-mediated retrograde transport in certain cells (By similarity). May recruit other proteins to membranes with high curvature. May promote membrane fusion (PubMed:11604418). Involved in activation of caspase-dependent apoptosis by promoting BAX/BAK1 activation (PubMed:16227588). Isoform 1 acts proapoptotic in fibroblasts (By similarity). Involved in caspase-independent apoptosis during nutrition starvation and involved in the regulation of autophagy. Activates lipid kinase activity of PIK3C3 during autophagy probably by associating with the PI3K complex II (PI3KC3-C2) (PubMed:17891140). Associated with PI3KC3-C2 during autophagy may regulate the trafficking of ATG9A from the Golgi complex to the peripheral cytoplasm for the formation of autophagosomes by inducing Golgi membrane tubulation and fragmentation (PubMed:21068542). Involved in regulation of degradative endocytic trafficking and cytokinesis, probably in the context of PI3KC3-C2 (PubMed:20643123). Isoform 2 acts antiapoptotic in neuronal cells; involved in maintenance of mitochondrial morphology and promotes neuronal viability (By similarity). {ECO:0000250|UniProtKB:Q9JK48, ECO:0000269|PubMed:11604418, ECO:0000269|PubMed:15452144, ECO:0000269|PubMed:17891140, ECO:0000269|PubMed:20643123, ECO:0000269|PubMed:21068542}.;
- Pathway
- Endocytosis - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Nanoparticle triggered autophagic cell death;Senescence and Autophagy in Cancer
(Consensus)
Recessive Scores
- pRec
- 0.131
Intolerance Scores
- loftool
- 0.208
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- 0.108
- hipred
- Y
- hipred_score
- 0.654
- ghis
- 0.563
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.862
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sh3glb1
- Phenotype
- cellular phenotype;
Gene ontology
- Biological process
- autophagy;apoptotic process;positive regulation of autophagy;regulation of macroautophagy;regulation of protein stability;positive regulation of protein oligomerization;regulation of cytokinesis;receptor catabolic process;cellular response to amino acid starvation;cellular response to glucose starvation;autophagic cell death;protein complex oligomerization;membrane fission;positive regulation of membrane tubulation;protein localization to vacuolar membrane;positive regulation of protein targeting to mitochondrion;positive regulation of autophagosome assembly
- Cellular component
- Golgi membrane;autophagosome membrane;cytoplasm;mitochondrial outer membrane;cytosol;midbody;cytoplasmic vesicle
- Molecular function
- protein binding;lipid binding;identical protein binding;protein homodimerization activity;cadherin binding