NSG1
Basic information
Region (hg38): 4:4348140-4419058
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 NSG1 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in NSG1
This is a list of pathogenic ClinVar variants found in the NSG1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-4387654-G-T | not specified | Uncertain significance (Jul 13, 2021) | ||
| 4-4391566-C-T | not specified | Uncertain significance (Nov 10, 2021) | ||
| 4-4409666-G-A | not specified | Uncertain significance (Sep 27, 2021) | ||
| 4-4417350-C-T | not specified | Uncertain significance (Aug 13, 2021) | ||
| 4-4417416-C-T | not specified | Uncertain significance (Oct 19, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NSG1 | protein_coding | protein_coding | ENST00000421177 | 4 | 70919 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00883 | 0.817 | 125729 | 0 | 19 | 125748 | 0.0000756 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.369 | 131 | 120 | 1.09 | 0.00000766 | 1202 |
| Missense in Polyphen | 41 | 46.953 | 0.87322 | 514 | ||
| Synonymous | 0.0593 | 55 | 55.6 | 0.990 | 0.00000403 | 367 |
| Loss of Function | 1.07 | 4 | 7.08 | 0.565 | 2.98e-7 | 91 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000120 | 0.000119 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000231 | 0.000231 |
| European (Non-Finnish) | 0.0000881 | 0.0000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in the recycling mechanism in neurons of multiple receptors, including AMPAR, APP and L1CAM and acts at the level of early endosomes to promote sorting of receptors toward a recycling pathway. Regulates sorting and recycling of GRIA2 through interaction with GRIP1 and then contributes to the regulation of synaptic transmission and plasticity by affecting the recycling and targeting of AMPA receptors to the synapse (By similarity). Is required for faithful sorting of L1CAM to axons by facilitating trafficking from somatodendritic early endosome or the recycling endosome (By similarity). In an other hand, induces apoptosis via the activation of CASP3 in response to DNA damage (PubMed:20599942, PubMed:20878061). {ECO:0000250|UniProtKB:P02683, ECO:0000250|UniProtKB:Q62092, ECO:0000269|PubMed:20599942, ECO:0000269|PubMed:20878061}.;
- Pathway
- p73 transcription factor network
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.69
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.398
- ghis
- 0.569
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nsg1
- Phenotype
Gene ontology
- Biological process
- receptor recycling;positive regulation of receptor recycling;apoptotic process;dopamine receptor signaling pathway;endosomal transport;amyloid precursor protein metabolic process;clathrin coat assembly;spontaneous synaptic transmission;neurotransmitter receptor transport, endosome to postsynaptic membrane;vesicle-mediated transport in synapse;neurotransmitter receptor cycle;postsynaptic neurotransmitter receptor cycle;regulation of long-term synaptic potentiation
- Cellular component
- nucleus;cytoplasm;endosome;late endosome;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;lateral plasma membrane;dendrite;cytoplasmic vesicle membrane;early endosome membrane;Golgi cisterna membrane;multivesicular body membrane;trans-Golgi network membrane;somatodendritic compartment;lysosomal lumen;postsynaptic membrane;recycling endosome membrane;postsynaptic endosome;glutamatergic synapse
- Molecular function
- signaling receptor binding;protein binding;clathrin light chain binding