LY6E

lymphocyte antigen 6 family member E, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 8:143017982-143023832

Links

ENSG00000160932 ∙ NCBI:4061 ∙ OMIM:601384 ∙ HGNC:6727 ∙ Uniprot:Q16553 ∙ 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 LY6E gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LY6E 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					2	2
missense			11	2	1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	3

Variants in LY6E

This is a list of pathogenic ClinVar variants found in the LY6E region.

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

Position	Type	Phenotype	Significance	ClinVar
8-143021314-C-T		not specified	Uncertain significance (Jul 09, 2024)
8-143021320-C-T		not specified	Uncertain significance (Jun 29, 2023)
8-143021327-G-T		not specified	Uncertain significance (Jan 09, 2025)
8-143021406-G-A		not specified	Uncertain significance (Aug 26, 2024)
8-143021602-C-G		not specified	Uncertain significance (Aug 04, 2024)
8-143021634-G-A		not specified	Likely benign (Jan 18, 2023)
8-143021655-A-T		not specified	Uncertain significance (Sep 16, 2021)
8-143021665-G-C		not specified	Uncertain significance (May 10, 2023)
8-143021695-G-A		not specified	Uncertain significance (Nov 11, 2024)
8-143021699-G-A			Benign (Mar 30, 2018)
8-143021703-G-A			Likely benign (Jun 05, 2018)
8-143021705-T-G		not specified	Uncertain significance (Mar 20, 2023)
8-143021708-C-T			Benign (Mar 29, 2018)
8-143021715-C-T		not specified	Uncertain significance (Dec 03, 2021)
8-143021718-G-C		not specified	Uncertain significance (Mar 20, 2023)
8-143021724-G-A			Benign (Mar 30, 2018)
8-143021764-C-T		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LY6E	protein_coding	protein_coding	ENST00000520466	3	5851

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.321	0.618	125702	0	4	125706	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.574	67	81.6	0.821	0.00000500	835
Missense in Polyphen		20	24.622	0.81229		273
Synonymous	-0.164	42	40.7	1.03	0.00000276	288
Loss of Function	1.45	1	4.21	0.238	2.62e-7	42

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in T-cell development. Believed to act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro inhibits alpha-3:beta-4-containing nAChRs maximum response. {ECO:0000250|UniProtKB:Q64253}.
• Pathway: Ectoderm Differentiation;Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.189

Intolerance Scores

• loftool: 0.267
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.187
• hipred: N
• hipred_score: 0.210
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.363

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ly6e
• Phenotype: 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); 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype; muscle phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway;negative regulation of signaling receptor activity
• Cellular component: extracellular region;plasma membrane;membrane;anchored component of membrane
• Molecular function: acetylcholine receptor inhibitor activity