NCS1
Basic information
Region (hg38): 9:130172404-130237303
Previous symbols: [ "FREQ" ]
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 NCS1 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 | 1 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 4 | 1 | 1 |
Variants in NCS1
This is a list of pathogenic ClinVar variants found in the NCS1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-130217928-C-A | Likely benign (Aug 21, 2018) | |||
| 9-130217953-G-A | not specified | Uncertain significance (Jun 18, 2024) | ||
| 9-130219765-C-T | not specified | Uncertain significance (Sep 26, 2022) | ||
| 9-130222698-A-G | not specified | Uncertain significance (Jun 17, 2024) | ||
| 9-130222748-C-T | Benign (Feb 25, 2018) | |||
| 9-130223091-G-A | not specified | Uncertain significance (Dec 28, 2023) | ||
| 9-130223167-G-T | Benign (Jan 23, 2018) | |||
| 9-130226473-G-C | not specified | Uncertain significance (Mar 06, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NCS1 | protein_coding | protein_coding | ENST00000372398 | 7 | 64727 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.664 | 0.335 | 125743 | 0 | 4 | 125747 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.22 | 43 | 108 | 0.399 | 0.00000679 | 1264 |
| Missense in Polyphen | 13 | 45.187 | 0.28769 | 512 | ||
| Synonymous | 0.972 | 40 | 48.6 | 0.823 | 0.00000368 | 343 |
| Loss of Function | 2.71 | 2 | 12.2 | 0.164 | 6.17e-7 | 141 |
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) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000655 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Neuronal calcium sensor, regulator of G protein-coupled receptor phosphorylation in a calcium dependent manner. Directly regulates GRK1 (RHOK), but not GRK2 to GRK5. Can substitute for calmodulin (By similarity). Stimulates PI4KB kinase activity (By similarity). Involved in long-term synaptic plasticity through its interaction with PICK1 (By similarity). May also play a role in neuron differentiation through inhibition of the activity of N- type voltage-gated calcium channel (By similarity). {ECO:0000250}.;
- Pathway
- regulation of ck1/cdk5 by type 1 glutamate receptors
(Consensus)
Recessive Scores
- pRec
- 0.186
Intolerance Scores
- loftool
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 42.88
Haploinsufficiency Scores
- pHI
- 0.187
- hipred
- Y
- hipred_score
- 0.693
- ghis
- 0.548
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.781
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Ncs1
- 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); vision/eye phenotype;
Gene ontology
- Biological process
- regulation of neuron projection development;positive regulation of exocytosis;phosphatidylinositol-mediated signaling;calcium ion transmembrane transport;regulation of presynaptic cytosolic calcium ion concentration;regulation of synaptic vesicle exocytosis
- Cellular component
- cytoplasm;Golgi apparatus;plasma membrane;postsynaptic density;cell junction;dendrite;dense core granule;intracellular membrane-bounded organelle;calyx of Held;postsynaptic membrane;perinuclear region of cytoplasm;glutamatergic synapse;presynaptic cytosol;postsynaptic cytosol
- Molecular function
- magnesium ion binding;voltage-gated calcium channel activity;calcium ion binding;protein binding;protein kinase binding;voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels