LY6G5B

Summary

LY6G5B (lymphocyte antigen 6 family member G5B, HGNC:13931) is a protein-coding gene on chromosome 6p21.33, encoding Lymphocyte antigen 6 complex locus protein G5b (Q8NDX9).

LY6G5B belongs to a cluster of leukocyte antigen-6 (LY6) genes located in the major histocompatibility complex (MHC) class III region on chromosome 6. Members of the LY6 superfamily typically contain 70 to 80 amino acids, including 8 to 10 cysteines. Most LY6 proteins are attached to the cell surface by a glycosylphosphatidylinositol (GPI) anchor that is directly involved in signal transduction (Mallya et al., 2002 [PubMed 12079290]).

Source: NCBI Gene 58496 — RefSeq curated summary.

At a glance

• GWAS associations: 24
• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_021221

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13931
Approved symbol	LY6G5B
Name	lymphocyte antigen 6 family member G5B
Location	6p21.33
Locus type	gene with protein product
Status	Approved
Aliases	G5b
Ensembl gene	ENSG00000240053
Ensembl biotype	protein_coding
OMIM	610433
Entrez	58496

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000375864, ENST00000409525, ENST00000471088

RefSeq mRNA: 1 — MANE Select: NM_021221 NM_021221

CCDS: CCDS34400

Canonical transcript exons

ENST00000375864 — 3 exons

Exon	Start	End
ENSE00003608174	31671156	31671284
ENSE00003654205	31671864	31673546
ENSE00003978212	31669976	31671008

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 93.56.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0903 / max 6.1207, expressed in 34 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
67021	0.0903	34

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	93.56	gold quality
cerebellar cortex	UBERON:0002129	93.38	gold quality
cerebellar hemisphere	UBERON:0002245	93.36	gold quality
cerebellum	UBERON:0002037	93.33	gold quality
skin of leg	UBERON:0001511	92.41	gold quality
mucosa of stomach	UBERON:0001199	92.31	gold quality
zone of skin	UBERON:0000014	91.86	gold quality
skin of abdomen	UBERON:0001416	91.22	gold quality
tibial nerve	UBERON:0001323	90.46	gold quality
left ovary	UBERON:0002119	90.17	gold quality
right ovary	UBERON:0002118	90.01	gold quality
subcutaneous adipose tissue	UBERON:0002190	89.70	gold quality
left uterine tube	UBERON:0001303	89.40	gold quality
granulocyte	CL:0000094	89.35	gold quality
small intestine Peyer’s patch	UBERON:0003454	89.22	gold quality
ovary	UBERON:0000992	89.20	gold quality
body of uterus	UBERON:0009853	89.16	gold quality
tibial artery	UBERON:0007610	89.05	gold quality
right lung	UBERON:0002167	89.04	gold quality
popliteal artery	UBERON:0002250	89.00	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	88.49	gold quality
muscle layer of sigmoid colon	UBERON:0035805	88.44	gold quality
lower esophagus muscularis layer	UBERON:0035833	88.39	gold quality
lower esophagus	UBERON:0013473	88.34	gold quality
spleen	UBERON:0002106	88.18	gold quality
small intestine	UBERON:0002108	88.15	gold quality
endocervix	UBERON:0000458	88.05	gold quality
transverse colon	UBERON:0001157	87.96	gold quality
thoracic mammary gland	UBERON:0005200	87.84	gold quality
adipose tissue	UBERON:0001013	87.73	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.52

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting LY6G5B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-609	99.82	64.26	505
HSA-MIR-7160-5P	99.11	67.17	2207
HSA-MIR-4801	98.96	69.42	2096
HSA-MIR-6804-5P	98.39	65.77	1084

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ly6g5b	ENSMUSG00000043807
rattus_norvegicus	Ly6g5b	ENSRNOG00000027516

Protein

Protein identifiers

Lymphocyte antigen 6 complex locus protein G5b — Q8NDX9 (reviewed: Q8NDX9)

All UniProt accessions (3): A0A1U9X7Y3, N0E641, Q8NDX9

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Forms oligomer.

Subcellular location. Secreted.

Post-translational modifications. N-glycosylated.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NDX9-1	1	yes
Q8NDX9-2	2

RefSeq proteins (1): NP_067044* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR016054	LY6_UPA_recep-like	Domain
IPR038773	LY6G5B	Family
IPR045860	Snake_toxin-like_sf	Homologous_superfamily

Pfam: PF00021

UniProt features (14 total): disulfide bond 5, sequence variant 3, glycosylation site 2, signal peptide 1, chain 1, splice variant 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NDX9-F1	76.66	0.36

Functional residue map

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

Disulfide bonds (5): 28–55, 31–40, 47–73, 81–98, 99–104

Glycosylation sites (2): 141, 183

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 25 (showing top): GOCC_CELL_SURFACE, WTGAAAT_UNKNOWN, OCT1_06, YNGTTNNNATT_UNKNOWN, MARSON_BOUND_BY_E2F4_UNSTIMULATED, GOCC_SIDE_OF_MEMBRANE, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_DN, LI_INDUCED_T_TO_NATURAL_KILLER_UP, GOCC_EXTERNAL_SIDE_OF_PLASMA_MEMBRANE, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_DN, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_UP, ZFHX3_TARGET_GENES, MIR6748_5P, MIR609, GSE7219_UNSTIM_VS_LPS_AND_ANTI_CD40_STIM_DC_DN

GO Biological Process (0):

GO Molecular Function (1): identical protein binding (GO:0042802)

GO Cellular Component (3): extracellular region (GO:0005576), external side of plasma membrane (GO:0009897), protein-containing complex (GO:0032991)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein binding	1
cellular anatomical structure	1
plasma membrane	1
cell surface	1
side of membrane	1
cellular_component	1

Protein interactions and networks

STRING

842 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LY6G5B	LY6G5C	Q5SRR4	730
LY6G5B	LY6G6C	O95867	695
LY6G5B	LY6L	H3BQJ8	658
LY6G5B	PATE3	B3GLJ2	641
LY6G5B	A0A0B4J1T7	A0A0B4J1T7	620
LY6G5B	LY6G6F	Q5SQ64	609
LY6G5B	CSNK2B	P07312	604
LY6G5B	PINLYP	A6NC86	599
LY6G5B	GPANK1	O95872	591
LY6G5B	PATE2	Q6UY27	582
LY6G5B	PATE4	P0C8F1	575
LY6G5B	LYPD5	Q6UWN5	574
LY6G5B	PATE1	Q8WXA2	571
LY6G5B	SPACA4	Q8TDM5	541
LY6G5B	ABHD16A	O95870	538

IntAct

3 interactions, top by confidence:

A	B	Type	Score
LY6G5B	POTEF	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350

BioGRID (27): LY6G5B (Affinity Capture-MS), LY6G5B (Affinity Capture-MS), LY6G5B (Synthetic Lethality), TEX15 (Affinity Capture-MS), MPZL1 (Affinity Capture-MS), RBPMS (Affinity Capture-MS), TUBB3 (Affinity Capture-MS), POTEF (Affinity Capture-MS), C17orf80 (Affinity Capture-MS), HELZ (Affinity Capture-MS), DCP2 (Affinity Capture-MS), SENP1 (Affinity Capture-MS), TUBB8 (Affinity Capture-MS), TBL1X (Affinity Capture-MS), ACTA2 (Affinity Capture-MS)

ESM2 similar proteins: A2VE33, D3ZF92, O43278, O55006, O55162, O75509, O88393, O89103, O95274, P10228, P26342, P35054, Q03167, Q05588, Q06175, Q06186, Q08E66, Q1RMT9, Q56A20, Q5DID3, Q5RCS3, Q61003, Q63961, Q6UWN5, Q7SXB3, Q7TMJ8, Q7TQN2, Q86T13, Q86VZ4, Q8BH27, Q8BHC0, Q8CB67, Q8K1T4, Q8NDX9, Q8VCP9, Q91YK8, Q91ZV2, Q91ZV3, Q924B5, Q96FE7

Diamond homologs: Q6MG53, Q8K1T4, Q8NDX9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	28
Likely benign	5
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

492 predictions. Top by Δscore:

Variant	Effect	Δscore
6:31671154:A:AG	acceptor_gain	1.0000
6:31671155:G:GA	acceptor_gain	1.0000
6:31671155:GTT:G	acceptor_gain	1.0000
6:31671155:GTTCC:G	acceptor_gain	1.0000
6:31671232:G:GT	donor_gain	1.0000
6:31671282:ATGGT:A	donor_loss	1.0000
6:31671285:GT:G	donor_loss	1.0000
6:31671286:T:A	donor_loss	1.0000
6:31671862:A:AG	acceptor_gain	1.0000
6:31671863:G:GG	acceptor_gain	1.0000
6:31670289:A:G	donor_gain	0.9900
6:31671145:T:A	acceptor_loss	0.9900
6:31671145:T:TA	acceptor_gain	0.9900
6:31671154:A:AC	acceptor_loss	0.9900
6:31671155:GT:G	acceptor_gain	0.9900
6:31671155:GTTC:G	acceptor_gain	0.9900
6:31671282:ATG:A	donor_loss	0.9900
6:31671283:TGGTA:T	donor_loss	0.9900
6:31671285:G:GG	donor_gain	0.9900
6:31671861:CA:C	acceptor_loss	0.9900
6:31671863:GAT:G	acceptor_gain	0.9900
6:31670266:A:T	donor_gain	0.9800
6:31671154:A:G	acceptor_loss	0.9800
6:31671863:GA:G	acceptor_gain	0.9800
6:31671863:GATGT:G	acceptor_gain	0.9800
6:31669988:G:GT	donor_gain	0.9700
6:31670265:G:GT	donor_gain	0.9700
6:31671295:TCCC:T	donor_gain	0.9700
6:31671860:TCAGA:T	acceptor_gain	0.9700
6:31671861:CAGA:C	acceptor_gain	0.9700

AlphaMissense

1293 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:31671878:T:C	F68L	0.979
6:31671880:C:A	F68L	0.979
6:31671880:C:G	F68L	0.979
6:31671997:G:C	W107C	0.964
6:31671997:G:T	W107C	0.964
6:31671879:T:C	F68S	0.951
6:31671885:T:A	V70D	0.946
6:31671879:T:G	F68C	0.928
6:31671893:T:A	C73S	0.919
6:31671894:G:C	C73S	0.919
6:31671956:T:G	Y94D	0.915
6:31671971:T:C	C99R	0.914
6:31671991:C:A	N105K	0.914
6:31671991:C:G	N105K	0.914
6:31671995:T:A	W107R	0.914
6:31671995:T:C	W107R	0.914
6:31671236:T:C	C47R	0.913
6:31671260:T:C	C55R	0.912
6:31671188:T:C	C31R	0.911
6:31671215:T:C	C40R	0.910
6:31671987:G:A	C104Y	0.910
6:31671893:T:C	C73R	0.908
6:31671917:T:A	C81S	0.908
6:31671918:G:C	C81S	0.908
6:31671972:G:A	C99Y	0.907
6:31671276:T:A	I60N	0.905
6:31671986:T:A	C104S	0.904
6:31671987:G:C	C104S	0.904
6:31671236:T:A	C47S	0.901
6:31671237:G:C	C47S	0.901

dbSNP variants (sampled 300 via entrez): RS1000010643 (6:31669921 C>T), RS1002874034 (6:31670103 G>A), RS1003363370 (6:31672525 A>C,G), RS1003415825 (6:31672771 A>G,T), RS1004541573 (6:31668958 A>C), RS1005110996 (6:31674007 C>T), RS1005331522 (6:31671201 A>T), RS1006217739 (6:31669538 A>G), RS1006330748 (6:31669740 A>G), RS1006445089 (6:31673988 C>T), RS1007361152 (6:31672471 G>A,C), RS1007503753 (6:31668431 C>T), RS1007557090 (6:31673326 C>G,T), RS1008014949 (6:31668889 G>A), RS1009691535 (6:31673594 C>T)

Disease associations

OMIM: gene MIM:610433 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

24 associations (top):

Study	Trait	p-value
GCST004131_25	Inflammatory bowel disease	2.000000e-31
GCST004133_79	Ulcerative colitis	5.000000e-65
GCST004521_114	Autism spectrum disorder or schizophrenia	3.000000e-17
GCST004521_117	Autism spectrum disorder or schizophrenia	3.000000e-15
GCST004521_126	Autism spectrum disorder or schizophrenia	2.000000e-10
GCST004521_154	Autism spectrum disorder or schizophrenia	3.000000e-08
GCST004521_17	Autism spectrum disorder or schizophrenia	2.000000e-12
GCST004521_209	Autism spectrum disorder or schizophrenia	5.000000e-16
GCST004521_211	Autism spectrum disorder or schizophrenia	5.000000e-15
GCST004521_213	Autism spectrum disorder or schizophrenia	5.000000e-13
GCST004521_224	Autism spectrum disorder or schizophrenia	5.000000e-10
GCST004521_227	Autism spectrum disorder or schizophrenia	4.000000e-12
GCST004521_265	Autism spectrum disorder or schizophrenia	7.000000e-14
GCST004521_281	Autism spectrum disorder or schizophrenia	5.000000e-09
GCST004521_45	Autism spectrum disorder or schizophrenia	2.000000e-16
GCST004521_70	Autism spectrum disorder or schizophrenia	8.000000e-20
GCST004521_81	Autism spectrum disorder or schizophrenia	1.000000e-14
GCST008916_111	Asthma	2.000000e-14
GCST008916_114	Asthma	1.000000e-09
GCST008916_30	Asthma	1.000000e-09
GCST008917_2	Asthma (childhood onset)	4.000000e-07
GCST008921_1	Asthma and major depressive disorder	2.000000e-16
GCST010725_43	Malaria	5.000000e-07
GCST010725_62	Malaria	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	increases expression	1
Leflunomide	decreases expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	increases expression	1
Doxorubicin	increases expression	1
Niclosamide	decreases expression	1
Smoke	decreases expression	1
Urethane	decreases expression	1
Cyclosporine	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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