LYNX1
Ly6/neurotoxin 1, the group of LY6/PLAUR domain containing
Basic information
Region (hg38): 8:142771196-142777810
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 LYNX1 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 | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 0 |
Variants in LYNX1
This is a list of pathogenic ClinVar variants found in the LYNX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-142775598-C-T | not specified | Uncertain significance (Mar 16, 2024) | ||
| 8-142775601-G-A | not specified | Uncertain significance (Aug 12, 2022) | ||
| 8-142775628-G-A | not specified | Uncertain significance (Mar 19, 2024) | ||
| 8-142775631-C-G | not specified | Uncertain significance (Dec 22, 2023) | ||
| 8-142775634-C-T | not specified | Uncertain significance (Jan 02, 2024) | ||
| 8-142775637-A-C | not specified | Uncertain significance (Jan 17, 2023) | ||
| 8-142775674-C-T | not specified | Uncertain significance (Feb 07, 2023) | ||
| 8-142775677-G-A | not specified | Uncertain significance (Jun 05, 2023) | ||
| 8-142775950-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
| 8-142775953-G-A | not specified | Uncertain significance (Jan 03, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LYNX1 | protein_coding | protein_coding | ENST00000335822 | 4 | 13889 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0263 | 0.802 | 125435 | 0 | 9 | 125444 | 0.0000359 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.973 | 57 | 81.8 | 0.697 | 0.00000467 | 831 |
| Missense in Polyphen | 13 | 22.468 | 0.57859 | 228 | ||
| Synonymous | 0.0529 | 35 | 35.4 | 0.989 | 0.00000245 | 253 |
| Loss of Function | 1.03 | 3 | 5.64 | 0.532 | 3.32e-7 | 57 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.000101 | 0.0000995 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000689 | 0.0000618 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000190 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Acts in different tissues through interaction to nicotinic acetylcholine receptors (nAChRs) (PubMed:21252236). The proposed role as modulator of nAChR activity seems to be dependent on the nAChR subtype and stoichiometry, and to involve an effect on nAChR trafficking and its cell surface expression, and on single channel properties of the nAChR inserted in the plasma membrane. Modulates functional properties of nicotinic acetylcholine receptors (nAChRs) to prevent excessive excitation, and hence neurodegeneration. Enhances desensitization by increasing both the rate and extent of desensitization of alpha- 4:beta-2-containing nAChRs and slowing recovery from desensitization. Promotes large amplitude ACh-evoked currents through alpha-4:beta-2 nAChRs. Is involved in regulation of the nAChR pentameric assembly in the endoplasmic reticulum. Shifts stoichiometry from high sensitivity alpha-4(2):beta-2(3) to low sensitivity alpha-4(3):beta-2(2) nAChR (By similarity). In vitro modulates alpha-3:beta-4-containing nAChRs. Reduces cell surface expression of (alpha-3:beta-4)(2):beta-4 and (alpha-3:beta- 4)(2):alpha-5 nAChRs suggesting an interaction with nAChR alpha- 3(-):(+)beta-4 subunit interfaces and an allosteric mode. Corresponding single channel effects characterized by decreased unitary conductance, altered burst proportions and enhanced desensitization/inactivation seem to depend on nAChR alpha:alpha subunit interfaces and are greater in (alpha-3:beta-2)(2):alpha-3 when compared to (alpha-3:beta-2)(2):alpha-5 nAChRs (PubMed:28100642). Prevents plasticity in the primary visual cortex late in life (By similarity). {ECO:0000250|UniProtKB:P0DP60, ECO:0000269|PubMed:21252236, ECO:0000269|PubMed:28100642}.;
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- loftool
- 0.667
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 34.6
Haploinsufficiency Scores
- pHI
- 0.0740
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.525
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.421
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lynx1
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- synaptic transmission, cholinergic;regulation of neurotransmitter receptor activity;negative regulation of signaling receptor activity
- Cellular component
- endoplasmic reticulum;plasma membrane;membrane;dendrite;anchored component of membrane
- Molecular function
- ion channel inhibitor activity;acetylcholine receptor regulator activity;acetylcholine receptor inhibitor activity;acetylcholine receptor binding