SH3GL2
SH3 domain containing GRB2 like 2, endophilin A1, the group of N-BAR domain containing
Basic information
Region (hg38): 9:17579066-17797124
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (33 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3GL2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003026.5. 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 | 1 | |||||
| missense | 33 | 33 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 33 | 0 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SH3GL2 | protein_coding | protein_coding | ENST00000380607 | 9 | 218048 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000119 | 0.991 | 125706 | 0 | 12 | 125718 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.963 | 153 | 190 | 0.804 | 0.00000961 | 2323 |
| Missense in Polyphen | 46 | 74.133 | 0.62051 | 925 | ||
| Synonymous | -2.04 | 89 | 67.6 | 1.32 | 0.00000353 | 642 |
| Loss of Function | 2.30 | 10 | 21.5 | 0.465 | 0.00000126 | 235 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000874 | 0.0000874 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000795 | 0.0000791 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Implicated in synaptic vesicle endocytosis. May recruit other proteins to membranes with high curvature. Required for BDNF-dependent dendrite outgrowth. Cooperates with SH3GL2 to mediate BDNF-NTRK2 early endocytic trafficking and signaling from early endosomes. {ECO:0000250|UniProtKB:Q62420}.;
- Pathway
- Endocytosis - Homo sapiens (human);EGF-EGFR Signaling Pathway;Developmental Biology;Golgi Associated Vesicle Biogenesis;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;Disease;trans-Golgi Network Vesicle Budding;Signal Transduction;Recycling pathway of L1;Vesicle-mediated transport;Membrane Trafficking;MHC class II antigen presentation;Infectious disease;Immune System;Adaptive Immune System;Retrograde neurotrophin signalling;EGFR downregulation;Signaling by EGFR;Clathrin-mediated endocytosis;Signaling by NTRK1 (TRKA);Signaling by NTRKs;EGFR1;Cargo recognition for clathrin-mediated endocytosis;L1CAM interactions;Axon guidance;Negative regulation of MET activity;Signaling by MET;Signaling by Receptor Tyrosine Kinases;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Internalization of ErbB1;RhoA signaling pathway;InlB-mediated entry of Listeria monocytogenes into host cell;Listeria monocytogenes entry into host cells
(Consensus)
Recessive Scores
- pRec
- 0.208
Intolerance Scores
- loftool
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.36
Haploinsufficiency Scores
- pHI
- 0.315
- hipred
- Y
- hipred_score
- 0.819
- ghis
- 0.624
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 | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sh3gl2
- 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); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype;
Gene ontology
- Biological process
- regulation of receptor internalization;signal transduction;central nervous system development;synaptic vesicle uncoating;antigen processing and presentation of exogenous peptide antigen via MHC class II;neuron projection development;negative regulation of epidermal growth factor receptor signaling pathway;lipid tube assembly;membrane organization;dendrite extension;membrane tubulation;membrane bending;vesicle scission;positive regulation of membrane tubulation;cellular response to brain-derived neurotrophic factor stimulus;regulation of clathrin-dependent endocytosis
- Cellular component
- Golgi membrane;early endosome;cytosol;plasma membrane;clathrin-coated endocytic vesicle membrane;synaptic vesicle membrane;neuronal cell body;perinuclear region of cytoplasm;basal dendrite;photoreceptor ribbon synapse;Schaffer collateral - CA1 synapse;hippocampal mossy fiber to CA3 synapse;glutamatergic synapse;presynaptic cytosol
- Molecular function
- protein binding;protein C-terminus binding;lipid binding;protein kinase binding;identical protein binding;protein homodimerization activity