LY96
lymphocyte antigen 96, the group of MD-2 related lipid recognition domain containing
Basic information
Region (hg38): 8:73991392-74029079
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 LY96 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 LY96
This is a list of pathogenic ClinVar variants found in the LY96 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-74004819-A-G | not specified | Uncertain significance (Dec 17, 2023) | ||
| 8-74010027-A-C | not specified | Uncertain significance (Oct 17, 2023) | ||
| 8-74010049-C-T | not specified | Uncertain significance (Nov 30, 2022) | ||
| 8-74010126-G-A | not specified | Uncertain significance (Nov 21, 2022) | ||
| 8-74029041-C-T | not specified | Uncertain significance (Nov 21, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LY96 | protein_coding | protein_coding | ENST00000284818 | 5 | 37736 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000742 | 0.527 | 125711 | 0 | 28 | 125739 | 0.000111 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.148 | 77 | 80.8 | 0.954 | 0.00000380 | 1046 |
| Missense in Polyphen | 25 | 30.607 | 0.81681 | 397 | ||
| Synonymous | 0.719 | 24 | 28.9 | 0.830 | 0.00000143 | 281 |
| Loss of Function | 0.535 | 7 | 8.70 | 0.804 | 4.50e-7 | 110 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000247 | 0.000242 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000381 | 0.000381 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000355 | 0.0000352 |
| Middle Eastern | 0.000381 | 0.000381 |
| South Asian | 0.000393 | 0.000392 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds bacterial lipopolysaccharide (LPS) (PubMed:17803912, PubMed:17569869). Cooperates with TLR4 in the innate immune response to bacterial lipopolysaccharide (LPS), and with TLR2 in the response to cell wall components from Gram- positive and Gram-negative bacteria (PubMed:11160242, PubMed:11593030). Enhances TLR4-dependent activation of NF-kappa-B (PubMed:10359581). Cells expressing both LY96 and TLR4, but not TLR4 alone, respond to LPS (PubMed:10359581). {ECO:0000269|PubMed:10359581, ECO:0000269|PubMed:11160242, ECO:0000269|PubMed:11593030, ECO:0000269|PubMed:17569869, ECO:0000269|PubMed:17803912}.;
- Pathway
- Pertussis - Homo sapiens (human);Toll-like receptor signaling pathway - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Pathogenic Escherichia coli infection - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Regulation of toll-like receptor signaling pathway;Pathogenic Escherichia coli infection;Fibrin Complement Receptor 3 Signaling Pathway;Toll-like Receptor Signaling Pathway;TLR NFkB;toll-like receptor pathway;Toll-Like Receptors Cascades;Ligand-dependent caspase activation;Caspase activation via extrinsic apoptotic signalling pathway;Innate Immune System;Immune System;Apoptosis;Programmed Cell Death;Adaptive Immune System;inactivation of gsk3 by akt causes accumulation of b-catenin in alveolar macrophages;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;TLR p38;Regulation of TLR by endogenous ligand;ER-Phagosome pathway;TLR ECSIT MEKK1 JNK;TLR ECSIT MEKK1 p38;TLR JNK;Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon;IKK complex recruitment mediated by RIP1;TRIF-mediated programmed cell death;TRAF6-mediated induction of TAK1 complex within TLR4 complex;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Endogenous TLR signaling
(Consensus)
Recessive Scores
- pRec
- 0.177
Intolerance Scores
- loftool
- rvis_EVS
- 0.46
- rvis_percentile_EVS
- 78.16
Haploinsufficiency Scores
- pHI
- 0.0920
- hipred
- N
- hipred_score
- 0.182
- ghis
- 0.431
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ly96
- Phenotype
- cellular phenotype; hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- toll-like receptor signaling pathway;MyD88-dependent toll-like receptor signaling pathway;MyD88-independent toll-like receptor signaling pathway;inflammatory response;cellular defense response;cell surface receptor signaling pathway;I-kappaB kinase/NF-kappaB signaling;lipopolysaccharide-mediated signaling pathway;positive regulation of lipopolysaccharide-mediated signaling pathway;response to lipopolysaccharide;detection of lipopolysaccharide;positive regulation of tumor necrosis factor production;negative regulation of MyD88-independent toll-like receptor signaling pathway;toll-like receptor 4 signaling pathway;TRIF-dependent toll-like receptor signaling pathway;innate immune response;necroptotic process;apoptotic signaling pathway
- Cellular component
- extracellular space;plasma membrane;endosome membrane;intrinsic component of plasma membrane;lipopolysaccharide receptor complex
- Molecular function
- lipopolysaccharide binding;lipopolysaccharide receptor activity;protein binding;coreceptor activity;Toll-like receptor 4 binding