LY6E

protein-coding

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

Gene summary

This gene belongs to the human Ly6 gene family and encodes a glycosylphosphatidyl-inositol (GPI)-anchored cell surface protein. The protein plays an important role in T cell physiology, oncogenesis and immunological regulation. The protein is also involved in modulation of viral infection by coronaviruses, SARS-CoV, MERS-CoV and SARS-CoV-2. [provided by RefSeq, Aug 2021]

MANE transcript

NM_002346.3

Inheritance

—

ClinVar variants

U:22B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr8:143,017,982-143,023,832

External References & Databases

Ensembl (ENSG00000160932)

Transcript & Mutation Effects

hg38 • Region Span ~5.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LY6E variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 20

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002346.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					2 clinvar	2
missense			19 clinvar	2 clinvar	1 clinvar	22
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	22	2	3	27

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 101 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002346.3	RefSeq	NP_002337.1	3	MANE Select
ENST00000292494.11	Ensembl	ENSP00000292494.6	3	MANE Select
NM_001127213.2	RefSeq	NP_001120685.1	3	Standard
ENST00000429120.6	Ensembl	ENSP00000414307.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ectoderm Differentiation
Post-translational modification: synthesis of GPI-anchored proteins
Post-translational protein modification
Metabolism of proteins

Biological Process

cell surface receptor signaling pathway
negative regulation of signaling receptor activity

Molecular Function

acetylcholine receptor inhibitor activity

Cellular Component

extracellular region
plasma membrane
membrane
anchored component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000520466
Coding exons: 3
Length: 5851
Individuals with no LoFs: 125702
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125706
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.574	67	81.6	0.821	0.00000500	835
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.189

Intolerance Scores

LoFtool: 0.267
RVIS EVS: 0.15
RVIS percentile EVS: 64.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.363

Gene Damage Prediction

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