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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 51.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_002346.3	NP_002337.1	3	yes	-
ENST00000292494.11	ENSP00000292494.6	3	yes	-
NM_001127213.2	NP_001120685.1	3	-	-
ENST00000429120.6	ENSP00000414307.2	3	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LY6E gene.

• not_specified (20 variants)
• not_provided (4 variants)

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. These statistics are base on transcript: NM_002346.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			19	2	1	22
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	21	2	3

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
		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

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

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