LY6G5C

Summary

LY6G5C (lymphocyte antigen 6 family member G5C, HGNC:13932) is a protein-coding gene on chromosome 6p21.33, encoding Lymphocyte antigen 6 complex locus protein G5c (Q5SRR4). May have a role in hematopoietic cell differentiation.

LY6G5C 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 80741 — RefSeq curated summary.

At a glance

• GWAS associations: 24
• Clinical variants (ClinVar): 15 total
• MANE Select transcript: NM_025262

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13932
Approved symbol	LY6G5C
Name	lymphocyte antigen 6 family member G5C
Location	6p21.33
Locus type	gene with protein product
Status	Approved
Aliases	G5c, NG33
Ensembl gene	ENSG00000204428
Ensembl biotype	protein_coding
OMIM	610434
Entrez	80741

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding_CDS_not_defined, 2 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000375863, ENST00000383237, ENST00000460141, ENST00000461572, ENST00000467098, ENST00000474395, ENST00000474678

RefSeq mRNA: 1 — MANE Select: NM_025262 NM_025262

CCDS: CCDS34401

Canonical transcript exons

ENST00000324540 — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 135 present calls, max score 90.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 1.8104 / max 25.0367, expressed in 955 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
72785	1.3730	754
72783	0.3052	131
72784	0.1321	48

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	90.00	gold quality
cerebellar hemisphere	UBERON:0002245	89.86	gold quality
thymus	UBERON:0002370	89.85	gold quality
cerebellar cortex	UBERON:0002129	89.51	gold quality
cerebellum	UBERON:0002037	89.38	gold quality
right testis	UBERON:0004534	88.59	gold quality
left testis	UBERON:0004533	87.90	gold quality
testis	UBERON:0000473	86.65	gold quality
putamen	UBERON:0001874	86.36	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.93	gold quality
granulocyte	CL:0000094	85.37	gold quality
caudate nucleus	UBERON:0001873	85.25	gold quality
nucleus accumbens	UBERON:0001882	84.37	gold quality
monocyte	CL:0000576	83.68	gold quality
leukocyte	CL:0000738	83.49	gold quality
blood	UBERON:0000178	83.26	gold quality
pituitary gland	UBERON:0000007	81.68	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.92	gold quality
right frontal lobe	UBERON:0002810	80.49	gold quality
adenohypophysis	UBERON:0002196	80.48	gold quality
brain	UBERON:0000955	79.36	gold quality
quadriceps femoris	UBERON:0001377	79.30	gold quality
anterior cingulate cortex	UBERON:0009835	79.08	gold quality
cortical plate	UBERON:0005343	79.07	gold quality
spleen	UBERON:0002106	78.60	gold quality
amygdala	UBERON:0001876	78.28	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	78.21	gold quality
temporal lobe	UBERON:0001871	78.08	gold quality
gastrocnemius	UBERON:0001388	78.07	gold quality
hypothalamus	UBERON:0001898	77.93	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-4850	no	21.87
E-ANND-3	no	1.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting LY6G5C, 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-8485	100.00	77.57	4731
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-5002-5P	99.76	70.84	1763
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-4797-5P	99.39	68.01	1354
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-887-5P	98.82	65.90	1347
HSA-MIR-6878-5P	98.49	67.91	2142
HSA-MIR-595	98.25	67.44	699
HSA-MIR-615-5P	98.10	63.76	591
HSA-MIR-6842-3P	98.07	66.33	1325
HSA-MIR-4446-3P	97.91	64.29	991
HSA-MIR-7113-5P	97.88	67.33	1735
HSA-MIR-30C-1-3P	97.80	66.36	1499
HSA-MIR-30C-2-3P	97.80	66.45	1499
HSA-MIR-6788-5P	97.80	66.41	1532
HSA-MIR-3652	97.71	65.43	1890

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ly6g5c	ENSMUSG00000034482
rattus_norvegicus	Ly6g5c	ENSRNOG00000000846

Protein

Protein identifiers

Lymphocyte antigen 6 complex locus protein G5c — Q5SRR4 (reviewed: Q5SRR4)

All UniProt accessions (4): A0A1U9X7Y6, Q5SRR4, F8WBQ4, H7BYB1

UniProt curated annotations — full annotation on UniProt →

Function. May have a role in hematopoietic cell differentiation.

Subunit / interactions. Forms oligomers.

Subcellular location. Secreted.

Tissue specificity. Detected in T-cell lines and fetal and adult lung.

Post-translational modifications. N-glycosylated.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5SRR4-1	1	yes
Q5SRR4-2	2
Q5SRR4-3	3

RefSeq proteins (1): NP_079538* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR016054	LY6_UPA_recep-like	Domain
IPR026110	LY6G5C	Family

Pfam: PF00021

UniProt features (10 total): disulfide bond 4, splice variant 2, signal peptide 1, chain 1, domain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5SRR4-F1	79.53	0.39

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 (4): 62–89, 65–74, 81–107, 134–139

Glycosylation sites (1): 96

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN, GOCC_CELL_SURFACE, RIZKI_TUMOR_INVASIVENESS_3D_DN, GOCC_SIDE_OF_MEMBRANE, GOCC_EXTERNAL_SIDE_OF_PLASMA_MEMBRANE, PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP, LHX9_TARGET_GENES, METTL14_TARGET_GENES, NFKBIA_TARGET_GENES, MIR8485, MIR4492, MIR3941, MIR4456, MIR6875_5P

GO Biological Process (0):

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

GO Cellular Component (4): extracellular region (GO:0005576), external side of plasma membrane (GO:0009897), protein-containing complex (GO:0032991), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
protein binding	1
plasma membrane	1
cell surface	1
side of membrane	1
cellular_component	1

Protein interactions and networks

STRING

448 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LY6G5C	LY6G6C	O95867	796
LY6G5C	LY6G5B	Q8NDX9	730
LY6G5C	ABHD16A	O95870	615
LY6G5C	LY6L	H3BQJ8	610
LY6G5C	PATE3	B3GLJ2	598
LY6G5C	PINLYP	A6NC86	577
LY6G5C	LY6G6F	Q5SQ64	570
LY6G5C	C6orf47	O95873	568
LY6G5C	PATE2	Q6UY27	548
LY6G5C	A0A0B4J1T7	A0A0B4J1T7	547
LY6G5C	CSNK2B	P07312	541
LY6G5C	LYPD5	Q6UWN5	530
LY6G5C	PATE4	P0C8F1	519
LY6G5C	GPANK1	O95872	518
LY6G5C	PATE1	Q8WXA2	516

IntAct

2 interactions, top by confidence:

A	B	Type	Score
LY6G5C	ITGAV	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): LY6G5C (Proximity Label-MS), LY6G5C (Proximity Label-MS), MESDC2 (Affinity Capture-MS), TUBB8 (Affinity Capture-MS), UBR1 (Affinity Capture-MS), ITGAV (Affinity Capture-MS), UBR4 (Affinity Capture-MS), DHRS4 (Affinity Capture-MS), ATP7A (Affinity Capture-MS), KCMF1 (Affinity Capture-MS), TEX15 (Affinity Capture-MS), ITGA8 (Affinity Capture-MS), SQSTM1 (Affinity Capture-MS), EOGT (Affinity Capture-MS)

ESM2 similar proteins: A0JNB3, A0JNL5, H2LID1, H3BJG9, O55186, O94772, O95867, P05533, P0CW02, P0CW03, P0DP59, P0DPQ9, P0DTL4, P13987, P27274, P35456, P35459, P35460, P35461, P46657, P47777, P49616, P51447, P57096, P58019, P83106, Q05588, Q14210, Q148C3, Q28216, Q28785, Q4R5M8, Q5R510, Q5SRR4, Q63317, Q64253, Q6UWN5, Q6UX82, Q6UXB3, Q7TQN2

Diamond homologs: Q5SRR4, Q863H0, Q8CHN2, Q8K1T5, Q9XSV5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	9
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

465 predictions. Top by Δscore:

Variant	Effect	Δscore
6:31679100:CTGTT:C	donor_gain	0.9500
6:31679264:CTTAC:C	acceptor_gain	0.9500
6:31677201:C:CT	acceptor_gain	0.9300
6:31677202:A:T	acceptor_gain	0.9300
6:31677226:T:TA	donor_gain	0.9300
6:31679099:A:AC	donor_gain	0.9200
6:31679100:C:CC	donor_gain	0.9200
6:31679217:T:C	acceptor_gain	0.9200
6:31677195:A:C	acceptor_gain	0.9100
6:31678462:T:A	donor_gain	0.9000
6:31679217:T:TC	acceptor_gain	0.8900
6:31679100:CT:C	donor_gain	0.8700
6:31679213:G:GC	acceptor_gain	0.8700
6:31677194:C:CT	acceptor_gain	0.8400
6:31679210:CAGG:C	acceptor_gain	0.8400
6:31679213:G:C	acceptor_gain	0.8400
6:31680245:CCACT:C	donor_loss	0.8300
6:31680246:CACTT:C	donor_loss	0.8300
6:31680247:ACTT:A	donor_loss	0.8300
6:31680248:CTT:C	donor_loss	0.8300
6:31680249:TTACC:T	donor_loss	0.8300
6:31680250:T:TC	donor_loss	0.8300
6:31680251:A:C	donor_loss	0.8300
6:31680252:C:CT	donor_loss	0.8300
6:31680244:GCCAC:G	donor_loss	0.8200
6:31680251:A:AC	donor_gain	0.8200
6:31680252:C:CC	donor_gain	0.8200
6:31679100:CTG:C	donor_gain	0.8000
6:31677121:C:CC	acceptor_gain	0.7800
6:31679093:CCACT:C	donor_loss	0.7800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000181067 (6:31679491 C>G), RS1000256018 (6:31676640 A>G), RS1000608145 (6:31676370 AC>A), RS1000637702 (6:31679211 A>G,T), RS1001912133 (6:31682047 A>AT), RS1001916948 (6:31681021 C>A,T), RS1002263245 (6:31681565 G>A,C), RS1002273140 (6:31681645 C>T), RS1003082997 (6:31676417 A>G), RS1004794330 (6:31676734 CAA>C), RS1005370686 (6:31678284 C>T), RS1005443916 (6:31678631 A>G), RS1006384641 (6:31682029 G>A), RS1006854090 (6:31676255 G>A), RS1007047427 (6:31679995 C>G,T)

Disease associations

OMIM: gene MIM:610434 | 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

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	increases abundance, increases expression, affects methylation	2
aristolochic acid I	increases expression	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
jinfukang	affects cotreatment, decreases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	increases expression	1
Sunitinib	decreases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Rotenone	decreases expression	1
Smoke	increases abundance, increases expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	increases expression	1
1-Methyl-4-phenylpyridinium	decreases expression	1
Okadaic Acid	increases expression	1
Particulate Matter	affects methylation, increases abundance	1

Clinical trials (associated diseases)

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