LY6L

Summary

LY6L (lymphocyte antigen 6 family member L, HGNC:52284) is a protein-coding gene on chromosome 8q24.3, encoding Lymphocyte antigen 6L (H3BQJ8).

Predicted to be located in side of membrane. Predicted to be active in plasma membrane.

Source: NCBI Gene 101928108 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001368160

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:52284
Approved symbol	LY6L
Name	lymphocyte antigen 6 family member L
Location	8q24.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000261667
Ensembl biotype	protein_coding
Entrez	101928108

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000562505, ENST00000927995, ENST00000927996

RefSeq mRNA: 1 — MANE Select: NM_001368160 NM_001368160

CCDS: CCDS94350

Canonical transcript exons

ENST00000562505 — 4 exons

Exon	Start	End
ENSE00002577474	143082425	143083486
ENSE00002600890	143080630	143080659
ENSE00002611968	143081036	143081126
ENSE00002626081	143081211	143081327

Expression profiles

Bgee: expression breadth broad, 18 present calls, max score 95.62.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0849 / max 68.0261, expressed in 27 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
91391	0.0784	26
91390	0.0066	2

Top tissues by expression

126 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	95.62	gold quality
adult mammalian kidney	UBERON:0000082	57.15	gold quality
kidney	UBERON:0002113	49.75	gold quality
cortex of kidney	UBERON:0001225	41.58	gold quality
metanephros cortex	UBERON:0010533	40.76	gold quality
lower esophagus mucosa	UBERON:0035834	38.84	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
sural nerve	UBERON:0015488	36.33	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
urinary bladder	UBERON:0001255	30.41	gold quality
prostate gland	UBERON:0002367	29.93	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
gall bladder	UBERON:0002110	29.46	gold quality
prefrontal cortex	UBERON:0000451	29.43	gold quality
monocyte	CL:0000576	29.34	gold quality
leukocyte	CL:0000738	29.18	gold quality
lymph node	UBERON:0000029	28.98	gold quality
liver	UBERON:0002107	28.85	gold quality
right lobe of thyroid gland	UBERON:0001119	28.62	gold quality
duodenum	UBERON:0002114	28.14	gold quality
primary visual cortex	UBERON:0002436	27.67	gold quality
placenta	UBERON:0001987	27.65	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	27.52	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.17

Regulation

Is transcription factor: no

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ly6l	ENSMUSG00000093626
mus_musculus		ENSMUSG00000122072
rattus_norvegicus	Ly6l	ENSRNOG00000048148
rattus_norvegicus		ENSRNOG00000076621

Paralogs (2): LY6H (ENSG00000176956), LY6S (ENSG00000291309)

Protein

Protein identifiers

Lymphocyte antigen 6L — H3BQJ8 (reviewed: H3BQJ8)

Alternative names: Lymphocyte antigen 6 complex locus protein L

All UniProt accessions (1): H3BQJ8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell membrane.

RefSeq proteins (1): NP_001355089* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR016054	LY6_UPA_recep-like	Domain
IPR045860	Snake_toxin-like_sf	Homologous_superfamily
IPR051445	LY6H/LY6L_nAChR_modulators	Family

Pfam: PF00021

UniProt features (8 total): disulfide bond 2, signal peptide 1, chain 1, propeptide 1, domain 1, lipid moiety-binding region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-H3BQJ8-F1	82.60	0.60

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 117

Disulfide bonds (2): 30–47, 103–108

Glycosylation sites (1): 27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 4 (showing top): GOCC_SIDE_OF_MEMBRANE, chr8q24, GREB1_TARGET_GENES, HE_LIM_SUN_FETAL_LUNG_C3_SCG3_POS_LYMPHATIC_ENDOTHELIAL_CELL

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (3): plasma membrane (GO:0005886), side of membrane (GO:0098552), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
membrane	2
cellular anatomical structure	2
cell periphery	1
leaflet of membrane bilayer	1

Protein interactions and networks

STRING

72 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LY6L	PATE3	B3GLJ2	761
LY6L	PINLYP	A6NC86	717
LY6L	PATE2	Q6UY27	697
LY6L	LYPD5	Q6UWN5	670
LY6L	PATE1	Q8WXA2	668
LY6L	LY6G5B	Q8NDX9	658
LY6L	PATE4	P0C8F1	644
LY6L	LYPD4	Q6UWN0	630
LY6L	SPACA4	Q8TDM5	629
LY6L	LY6G6F	Q5SQ64	621
LY6L	LY6G5C	Q5SRR4	610
LY6L	LY6G6C	O95867	603
LY6L	LYPD2	Q6UXB3	593
LY6L	GML	Q99445	571
LY6L	TEX101	Q9BY14	570

IntAct

2 interactions, top by confidence:

A	B	Type	Score
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350

BioGRID (1): LOC101928108 (Affinity Capture-MS)

ESM2 similar proteins: A0JNB3, A0JNL5, A6NC86, H3BJG9, H3BQJ8, O55186, O94772, O95867, P05533, P0CW02, P0CW03, P0DTL4, P13987, P35456, P35459, P35460, P35461, P46657, P47777, P49616, P57096, P58019, Q03405, Q05588, Q14210, Q148C3, Q28216, Q28785, Q32PB3, Q4R5M8, Q5R510, Q63317, Q64253, Q6UWN5, Q6UX82, Q80ZQ0, Q8K1T6, Q8SQ46, Q8TDM5, Q924B5

Diamond homologs: H3BJG9, H3BQJ8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

0 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

531 predictions. Top by Δscore:

Variant	Effect	Δscore
8:143080627:G:GT	donor_gain	1.0000
8:143080653:A:T	donor_gain	1.0000
8:143081126:GGT:G	donor_loss	1.0000
8:143081128:T:A	donor_loss	1.0000
8:143081328:G:GG	donor_gain	1.0000
8:143080649:C:T	donor_gain	0.9900
8:143080652:G:GT	donor_gain	0.9900
8:143080656:GAAG:G	donor_gain	0.9900
8:143080657:A:T	donor_gain	0.9900
8:143080657:AAG:A	donor_loss	0.9900
8:143080660:G:GA	donor_loss	0.9900
8:143080661:T:A	donor_loss	0.9900
8:143080666:G:GT	donor_gain	0.9900
8:143081031:CTCAG:C	acceptor_loss	0.9900
8:143081033:CA:C	acceptor_loss	0.9900
8:143081034:A:AG	acceptor_gain	0.9900
8:143081034:AGG:A	acceptor_loss	0.9900
8:143081034:AGGCT:A	acceptor_gain	0.9900
8:143081035:G:GG	acceptor_gain	0.9900
8:143081035:G:T	acceptor_loss	0.9900
8:143081035:GGCT:G	acceptor_gain	0.9900
8:143081035:GGCTG:G	acceptor_gain	0.9900
8:143081091:T:A	acceptor_gain	0.9900
8:143081208:CA:C	acceptor_loss	0.9900
8:143081209:A:AG	acceptor_gain	0.9900
8:143081209:AG:A	acceptor_loss	0.9900
8:143081210:G:GG	acceptor_gain	0.9900
8:143081210:GCTC:G	acceptor_gain	0.9900
8:143081316:T:TA	donor_gain	0.9900
8:143081323:TTTTA:T	donor_gain	0.9900

AlphaMissense

887 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:143082498:G:C	W88C	0.987
8:143082498:G:T	W88C	0.987
8:143081238:T:G	F34C	0.985
8:143081297:T:A	C54S	0.984
8:143081298:G:C	C54S	0.984
8:143081237:T:C	F34L	0.983
8:143081239:C:A	F34L	0.983
8:143081239:C:G	F34L	0.983
8:143082453:A:C	K73N	0.980
8:143082453:A:T	K73N	0.980
8:143082448:A:C	S72R	0.977
8:143082450:C:A	S72R	0.977
8:143082450:C:G	S72R	0.977
8:143082452:A:T	K73I	0.972
8:143082469:T:A	C79S	0.970
8:143082470:G:C	C79S	0.970
8:143081261:T:A	C42S	0.969
8:143081262:G:C	C42S	0.969
8:143081299:C:G	C54W	0.968
8:143081234:T:A	C33S	0.967
8:143081235:G:C	C33S	0.967
8:143081298:G:A	C54Y	0.967
8:143081303:T:C	S56P	0.967
8:143081297:T:C	C54R	0.966
8:143082457:T:A	C75S	0.966
8:143082458:G:C	C75S	0.966
8:143082561:C:A	N109K	0.965
8:143082561:C:G	N109K	0.965
8:143082448:A:T	S72C	0.964
8:143082556:T:A	C108S	0.962

dbSNP variants (sampled 300 via entrez): RS1000036362 (8:143079910 G>C), RS1000845350 (8:143081856 T>C), RS1001293971 (8:143079415 G>A), RS1001528407 (8:143082139 A>G), RS1001682711 (8:143079125 G>A,T), RS1002127965 (8:143082971 A>T), RS1002191326 (8:143083931 G>A), RS1003388784 (8:143082149 G>T), RS1003866025 (8:143080565 G>A,C), RS1003933126 (8:143080332 G>A,T), RS1004302842 (8:143082753 C>A), RS1005028799 (8:143081512 T>A,G), RS1005611632 (8:143078850 C>T), RS1005691438 (8:143083418 G>A), RS1006378508 (8:143083117 G>A,C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.