SH3GL3
SH3 domain containing GRB2 like 3, endophilin A3, the group of N-BAR domain containing
Basic information
Region (hg38): 15:83447228-83618743
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 SH3GL3 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 | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 0 |
Variants in SH3GL3
This is a list of pathogenic ClinVar variants found in the SH3GL3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 15-83559296-A-G | not specified | Uncertain significance (Sep 14, 2023) | ||
| 15-83559298-G-A | not specified | Uncertain significance (Jan 19, 2024) | ||
| 15-83565138-T-C | not specified | Uncertain significance (Sep 13, 2023) | ||
| 15-83568582-G-T | not specified | Uncertain significance (Nov 26, 2024) | ||
| 15-83568651-C-G | not specified | Uncertain significance (Jul 31, 2024) | ||
| 15-83568655-G-A | not specified | Uncertain significance (Dec 21, 2023) | ||
| 15-83572643-A-T | not specified | Uncertain significance (Jun 17, 2024) | ||
| 15-83572691-A-T | not specified | Uncertain significance (Sep 04, 2024) | ||
| 15-83576652-C-T | not specified | Uncertain significance (Aug 19, 2024) | ||
| 15-83576674-C-T | not specified | Uncertain significance (Jul 12, 2022) | ||
| 15-83576716-G-T | not specified | Uncertain significance (Nov 24, 2024) | ||
| 15-83587025-T-A | not specified | Uncertain significance (Mar 20, 2023) | ||
| 15-83588697-A-G | not specified | Uncertain significance (Sep 16, 2021) | ||
| 15-83588724-C-G | not specified | Uncertain significance (Aug 12, 2021) | ||
| 15-83618084-T-C | not specified | Uncertain significance (Jun 28, 2024) | ||
| 15-83618087-A-G | not specified | Uncertain significance (May 22, 2023) | ||
| 15-83618106-C-A | not specified | Uncertain significance (Oct 07, 2024) | ||
| 15-83618217-G-A | Uncertain significance (Oct 01, 2018) | |||
| 15-83618221-G-T | not specified | Uncertain significance (Nov 18, 2022) | ||
| 15-83618270-G-T | not specified | Uncertain significance (Jul 06, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SH3GL3 | protein_coding | protein_coding | ENST00000427482 | 9 | 171516 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000102 | 0.988 | 125707 | 0 | 41 | 125748 | 0.000163 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.21 | 138 | 184 | 0.750 | 0.00000975 | 2270 |
| Missense in Polyphen | 64 | 89.281 | 0.71684 | 1083 | ||
| Synonymous | -0.762 | 79 | 70.8 | 1.12 | 0.00000431 | 630 |
| Loss of Function | 2.24 | 10 | 21.1 | 0.474 | 0.00000125 | 248 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000423 | 0.000416 |
| Ashkenazi Jewish | 0.0000996 | 0.0000992 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000163 | 0.000158 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.000200 | 0.000196 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Implicated in endocytosis. May recruit other proteins to membranes with high curvature (By similarity). {ECO:0000250}.;
- Pathway
- Endocytosis - Homo sapiens (human);EGF-EGFR Signaling Pathway;Disease;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Infectious disease;EGFR downregulation;Signaling by EGFR;Clathrin-mediated endocytosis;EGFR1;Cargo recognition for clathrin-mediated endocytosis;Negative regulation of MET activity;Signaling by MET;Signaling by Receptor Tyrosine Kinases;InlB-mediated entry of Listeria monocytogenes into host cell;Listeria monocytogenes entry into host cells
(Consensus)
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.660
- rvis_EVS
- 0.28
- rvis_percentile_EVS
- 71.27
Haploinsufficiency Scores
- pHI
- 0.0858
- hipred
- Y
- hipred_score
- 0.714
- ghis
- 0.437
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.860
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sh3gl3
- Phenotype
- normal 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- sh3gl3b
- Affected structure
- blood cell
- Phenotype tag
- abnormal
- Phenotype quality
- accumulation
Gene ontology
- Biological process
- endocytosis;signal transduction;central nervous system development;positive regulation of neuron differentiation;negative regulation of clathrin-dependent endocytosis
- Cellular component
- acrosomal vesicle;early endosome membrane;presynapse;postsynaptic endosome;glutamatergic synapse;postsynaptic density, intracellular component
- Molecular function
- protein binding;protein C-terminus binding;lipid binding;identical protein binding