LY86

lymphocyte antigen 86, the group of MD-2 related lipid recognition domain containing

Basic information

Region (hg38): 6:6588108-6654983

Links

ENSG00000112799 ∙ NCBI:9450 ∙ OMIM:605241 ∙ HGNC:16837 ∙ Uniprot:O95711 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LY86 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LY86 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	1
missense			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	2

Variants in LY86

This is a list of pathogenic ClinVar variants found in the LY86 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-6588741-G-T		not specified	Uncertain significance (Aug 08, 2022)
6-6588764-C-T			Benign (Apr 10, 2018)
6-6588822-C-A		not specified	Uncertain significance (Apr 23, 2024)
6-6588843-G-A		not specified	Uncertain significance (Mar 29, 2023)
6-6624971-A-C		not specified	Uncertain significance (Sep 01, 2021)
6-6625004-T-G		not specified	Uncertain significance (Apr 26, 2024)
6-6626346-T-C			Benign (Apr 10, 2018)
6-6649628-A-G		not specified	Uncertain significance (Feb 02, 2024)
6-6649629-G-T		not specified	Uncertain significance (Jan 08, 2024)
6-6649634-A-G		not specified	Uncertain significance (Mar 28, 2022)
6-6649672-C-T		not specified	Uncertain significance (May 27, 2022)
6-6654574-A-G		not specified	Uncertain significance (Aug 23, 2021)
6-6654583-C-T		not specified	Uncertain significance (Jul 13, 2021)
6-6654584-G-A		not specified	Uncertain significance (Mar 30, 2024)
6-6654584-G-C		not specified	Uncertain significance (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LY86	protein_coding	protein_coding	ENST00000379953	5	66876

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000225	0.305	125659	0	85	125744	0.000338

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.342	94	85.1	1.10	0.00000448	1042
Missense in Polyphen		36	31.518	1.1422		396
Synonymous	-0.475	37	33.5	1.10	0.00000206	305
Loss of Function	-0.00907	7	6.97	1.00	2.93e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00203	0.00199
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000139	0.000123
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.000504	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May cooperate with CD180 and TLR4 to mediate the innate immune response to bacterial lipopolysaccharide (LPS) and cytokine production. Important for efficient CD180 cell surface expression (By similarity). {ECO:0000250}.
• Pathway: Toll-Like Receptors Cascades;Innate Immune System;Immune System;Toll Like Receptor 4 (TLR4) Cascade (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.792
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.12

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.146
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.853

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ly86
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: apoptotic process;inflammatory response;humoral immune response;cell population proliferation;positive regulation of lipopolysaccharide-mediated signaling pathway;innate immune response
• Cellular component: extracellular space;plasma membrane
• Molecular function: protein binding