LYG2

Summary

LYG2 (lysozyme g2, HGNC:29615) is a protein-coding gene on chromosome 2q11.2, encoding Lysozyme g-like protein 2 (Q86SG7). May act as a potent antibacterial protein that may play a role in the innate immunity.

The protein encoded by this gene contains a SLT domain, a protein domain present in bacterial lytic transglycosylase (SLT) and in eukaryotic lysozymes (GEWL). SLT domain catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyglucosamine (GlcNAc).

Source: NCBI Gene 254773 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_175735

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29615
Approved symbol	LYG2
Name	lysozyme g2
Location	2q11.2
Locus type	gene with protein product
Status	Approved
Aliases	LYGH, LYGA2
Ensembl gene	ENSG00000185674
Ensembl biotype	protein_coding
OMIM	616547
Entrez	254773

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000333017, ENST00000409679, ENST00000423306, ENST00000423800, ENST00000924907

RefSeq mRNA: 1 — MANE Select: NM_175735 NM_175735

CCDS: CCDS2042

Canonical transcript exons

ENST00000333017 — 7 exons

Exon	Start	End
ENSE00001293661	99245262	99245458
ENSE00001305670	99254218	99254285
ENSE00001311068	99246680	99246820
ENSE00001311905	99243999	99244137
ENSE00001578565	99242246	99242482
ENSE00001714965	99255020	99255137
ENSE00003928691	99255603	99255666

Expression profiles

Bgee: expression breadth ubiquitous, 152 present calls, max score 89.52.

Top tissues by expression

244 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	89.52	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.09	gold quality
buccal mucosa cell	CL:0002336	78.00	silver quality
tendon of biceps brachii	UBERON:0008188	63.56	gold quality
cerebellar cortex	UBERON:0002129	59.89	gold quality
cerebellar hemisphere	UBERON:0002245	59.78	gold quality
cerebellum	UBERON:0002037	58.64	gold quality
right hemisphere of cerebellum	UBERON:0014890	58.15	gold quality
stromal cell of endometrium	CL:0002255	56.71	gold quality
tendon	UBERON:0000043	55.42	silver quality
monocyte	CL:0000576	54.59	gold quality
adenohypophysis	UBERON:0002196	53.91	gold quality
skin of abdomen	UBERON:0001416	53.34	gold quality
leukocyte	CL:0000738	53.18	gold quality
corpus callosum	UBERON:0002336	52.90	gold quality
lower lobe of lung	UBERON:0008949	52.63	silver quality
nucleus accumbens	UBERON:0001882	51.91	gold quality
pituitary gland	UBERON:0000007	51.61	gold quality
calcaneal tendon	UBERON:0003701	51.01	silver quality
medial globus pallidus	UBERON:0002477	50.71	gold quality
zone of skin	UBERON:0000014	50.63	gold quality
trabecular bone tissue	UBERON:0002483	50.41	gold quality
granulocyte	CL:0000094	50.11	silver quality
apex of heart	UBERON:0002098	49.96	gold quality
cortex of kidney	UBERON:0001225	49.87	gold quality
right lobe of thyroid gland	UBERON:0001119	49.86	gold quality
ganglionic eminence	UBERON:0004023	49.84	gold quality
left testis	UBERON:0004533	49.06	gold quality
right testis	UBERON:0004534	48.93	gold quality
skin of leg	UBERON:0001511	48.91	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.85

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

3 targeting LYG2, 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-433-3P	99.98	69.37	1203
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-4303	98.01	68.13	2304

Literature-anchored findings (GeneRIF, showing 2)

• HLysG2 is a potent antibacterial protein that may play a role in the innate immunity of the human eye. (PMID:21093056)
• HLysG2 was identified and purified from human seminal plasma and showed a significant killing effect on Micrococcus lysodeikticus, Bacillus subtilis and Staphylococcus aureus. (PMID:28274309)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lygl1	ENSDARG00000056874
danio_rerio	zgc:162941	ENSDARG00000071701
danio_rerio	lygl2	ENSDARG00000099562
mus_musculus	Lyg2	ENSMUSG00000061584
rattus_norvegicus	Lyg2	ENSRNOG00000050591

Paralogs (1): LYG1 (ENSG00000144214)

Protein

Protein identifiers

Lysozyme g-like protein 2 — Q86SG7 (reviewed: Q86SG7)

All UniProt accessions (3): C9J4J0, C9JBA4, Q86SG7

UniProt curated annotations — full annotation on UniProt →

Function. May act as a potent antibacterial protein that may play a role in the innate immunity.

Subcellular location. Secreted.

Tissue specificity. Strong expression detected in the eye and weak expression in the testis. No expression is observed in any other tissues.

Similarity. Belongs to the glycosyl hydrolase 23 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86SG7-1	1	yes
Q86SG7-2	2

RefSeq proteins (1): NP_783862* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002152	Glyco_hydro_23	Family
IPR023346	Lysozyme-like_dom_sf	Homologous_superfamily

Enzyme classification (BRENDA):

• EC 3.2.1.17 — lysozyme (BRENDA: 110 organisms, 187 substrates, 100 inhibitors, 8 Km, 2 kcat entries)

Substrate kinetics (BRENDA)

3 substrates with measured Km, best-characterized 3. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
4-METHYLUMBELLIFERYL-BETA-D-N,N’,N’’-TRIACETYLCH	0.0008–0.001	2
P-NITROPHENYL-N,N’,N’’,N’’’,N’’’’-PENTAACETYLCHI	8.33	1
P-NITROPHENYL-GLCNACBETA(1-4)GLCNACBETA(1-4)GLCN	—	0

UniProt features (10 total): sequence conflict 4, disulfide bond 2, signal peptide 1, chain 1, active site 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86SG7-F1	88.11	0.79

Functional residue map

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

Catalytic / active sites (1): 105

Disulfide bonds (2): 39–92, 53–61

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 36 (showing top): GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, AREB6_01, TGACCTY_ERR1_Q2, LHX3_01, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_AMINOGLYCAN_METABOLIC_PROCESS, GOBP_DEFENSE_RESPONSE_TO_GRAM_POSITIVE_BACTERIUM, GOBP_DEFENSE_RESPONSE_TO_BACTERIUM, GOBP_AMINOGLYCAN_CATABOLIC_PROCESS, TGGAAA_NFAT_Q4_01, GOMF_LYSOZYME_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_GLYCOSYL_BONDS, GOBP_RESPONSE_TO_BACTERIUM, chr2q11

GO Biological Process (3): peptidoglycan catabolic process (GO:0009253), defense response to bacterium (GO:0042742), defense response to Gram-positive bacterium (GO:0050830)

GO Molecular Function (4): lysozyme activity (GO:0003796), protein binding (GO:0005515), hydrolase activity (GO:0016787), hydrolase activity, acting on glycosyl bonds (GO:0016798)

GO Cellular Component (1): extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
peptidoglycan metabolic process	1
glycosaminoglycan catabolic process	1
defense response	1
response to bacterium	1
defense response to bacterium	1
hydrolase activity, hydrolyzing O-glycosyl compounds	1
peptidoglycan muralytic activity	1
binding	1
catalytic activity	1
hydrolase activity	1
cellular anatomical structure	1

Protein interactions and networks

STRING

724 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LYG2	BPIFB2	Q8N4F0	660
LYG2	ZNF696	Q9H7X3	516
LYG2	SERPINB10	P48595	511
LYG2	CLEC2A	Q6UVW9	490
LYG2	IFIT5	Q13325	485
LYG2	KRABD3	A5PL33	472
LYG2	KCNJ12	Q14500	422
LYG2	LYZL2	Q7Z4W2	411
LYG2	TMPRSS5	Q9H3S3	394
LYG2	ANKRD23	Q86SG2	381
LYG2	TTC16	Q8NEE8	377
LYG2	ADAMTSL2	Q86TH1	372
LYG2	KCNJ18	B7U540	349
LYG2	ACOD1	A6NK06	345
LYG2	GATD3	P0DPI2	342

IntAct

71 interactions, top by confidence:

A	B	Type	Score
OAZ3	AZIN1	psi-mi:“MI:0914”(association)	0.800
IFT43	TULP3	psi-mi:“MI:0914”(association)	0.790
KIF3A	KIF3C	psi-mi:“MI:0914”(association)	0.730
ANXA9	PPL	psi-mi:“MI:0914”(association)	0.660
RAB11B	SH3BP5	psi-mi:“MI:0914”(association)	0.640
CAPZA2	CNOT1	psi-mi:“MI:0914”(association)	0.640
LYG2	TEPSIN	psi-mi:“MI:0915”(physical association)	0.560
RPN2	SMPD2	psi-mi:“MI:0914”(association)	0.530
CPLX3	CIAO1	psi-mi:“MI:0914”(association)	0.530
LACC1	DUSP14	psi-mi:“MI:0914”(association)	0.530
NSMAF	DUSP14	psi-mi:“MI:0914”(association)	0.530
MRPL38	DUSP14	psi-mi:“MI:0914”(association)	0.530
FBXL4	DUSP14	psi-mi:“MI:0914”(association)	0.530
LYG2	COL4A2	psi-mi:“MI:0914”(association)	0.530
SEMG2	VSIG8	psi-mi:“MI:0914”(association)	0.530
DOLPP1	VSIG8	psi-mi:“MI:0914”(association)	0.530
APIP	VSIG8	psi-mi:“MI:0914”(association)	0.530
LYG2	TRAF2	psi-mi:“MI:0914”(association)	0.530
SIDT2	AP3D1	psi-mi:“MI:0914”(association)	0.530
LYG2	H2BC21	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (87): LYG2 (Affinity Capture-MS), LYG2 (Affinity Capture-MS), LYG2 (Affinity Capture-MS), LYG2 (Affinity Capture-MS), LYG2 (Affinity Capture-MS), LYG2 (Affinity Capture-MS), NID2 (Affinity Capture-MS), SPATA20 (Affinity Capture-MS), LYG2 (Affinity Capture-MS), LYG2 (Affinity Capture-MS), LYG2 (Affinity Capture-MS), VPS33B (Affinity Capture-MS), VIPAS39 (Affinity Capture-MS), LYG2 (Affinity Capture-MS), LYG2 (Affinity Capture-MS)

ESM2 similar proteins: B3A003, C0HLB7, C1IIX1, D9J142, D9J143, O02119, O04138, O22841, O22842, O24603, O76357, O76358, P05105, P16579, P19171, P21226, P27054, P29022, P29023, P29059, P29615, P36907, P37160, P37161, P42820, P48816, P50717, P50718, P52403, P52404, P52405, P80052, P83673, P86383, P86473, Q05538, Q1XG90, Q39799, Q41596, Q54F36

Diamond homologs: B3A0P5, G3XDD8, P00717, P00718, P00719, P27042, P61133, Q3V1I0, Q7LZR3, Q86SG7, Q8JFR1, Q90VZ3, Q90X99, Q9D7Q0, Q8N1E2, O31976, O64046

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	35
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

478 predictions. Top by Δscore:

Variant	Effect	Δscore
2:99242479:CCAC:C	acceptor_gain	1.0000
2:99242480:CACC:C	acceptor_gain	1.0000
2:99244134:CAAG:C	acceptor_gain	1.0000
2:99245329:T:A	donor_gain	1.0000
2:99246678:A:AC	donor_gain	1.0000
2:99246679:C:CC	donor_gain	1.0000
2:99246679:CCG:C	donor_gain	1.0000
2:99242480:CAC:C	acceptor_gain	0.9900
2:99242483:C:CC	acceptor_gain	0.9900
2:99242484:T:A	acceptor_loss	0.9900
2:99244133:TCAAG:T	acceptor_gain	0.9900
2:99244134:CAAGC:C	acceptor_gain	0.9900
2:99244138:C:CC	acceptor_gain	0.9900
2:99245330:C:A	donor_gain	0.9900
2:99246673:CACT:C	donor_loss	0.9900
2:99246674:ACTTA:A	donor_loss	0.9900
2:99246675:CTT:C	donor_loss	0.9900
2:99246676:TTAC:T	donor_loss	0.9900
2:99246677:T:TG	donor_loss	0.9900
2:99246679:CCGCA:C	donor_gain	0.9900
2:99246821:C:CA	acceptor_loss	0.9900
2:99246821:C:CC	acceptor_gain	0.9900
2:99242478:ACCAC:A	acceptor_gain	0.9800
2:99242479:CCACC:C	acceptor_gain	0.9800
2:99242481:AC:A	acceptor_gain	0.9800
2:99242482:CC:C	acceptor_gain	0.9800
2:99242488:A:AC	acceptor_gain	0.9800
2:99244135:AAGC:A	acceptor_loss	0.9800
2:99244136:AGCT:A	acceptor_loss	0.9800
2:99244137:GCTA:G	acceptor_loss	0.9800

AlphaMissense

1404 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:99242393:C:G	A204P	0.987
2:99245325:G:C	S106R	0.987
2:99245325:G:T	S106R	0.987
2:99245327:T:G	S106R	0.987
2:99245274:A:C	F123L	0.976
2:99245274:A:T	F123L	0.976
2:99245276:A:G	F123L	0.976
2:99242395:C:G	R203P	0.974
2:99242385:G:C	F206L	0.972
2:99242385:G:T	F206L	0.972
2:99242387:A:G	F206L	0.972
2:99245345:C:G	A100P	0.969
2:99242392:G:T	A204D	0.968
2:99245434:G:T	A70D	0.968
2:99245347:G:T	A99E	0.965
2:99245269:A:G	L125S	0.964
2:99244030:G:C	F163L	0.963
2:99244030:G:T	F163L	0.963
2:99244032:A:G	F163L	0.963
2:99244085:A:G	L145P	0.961
2:99245381:C:A	G88W	0.961
2:99242479:C:T	G175D	0.960
2:99245336:A:G	S103P	0.960
2:99245344:G:T	A100D	0.959
2:99242384:A:C	Y207D	0.956
2:99245272:C:T	G124D	0.956
2:99244004:A:G	L172P	0.955
2:99245335:G:A	S103F	0.955
2:99242367:G:C	F212L	0.953
2:99242367:G:T	F212L	0.953

dbSNP variants (sampled 300 via entrez): RS1000115499 (2:99262063 A>G), RS1000371968 (2:99259727 A>G), RS1000424411 (2:99260216 G>A), RS1000715066 (2:99261458 C>G,T), RS1000767528 (2:99261836 G>T), RS1000983730 (2:99248216 G>C,T), RS1001036321 (2:99248639 C>G,T), RS1001131366 (2:99247723 T>G), RS1001184117 (2:99247437 GTTTT>G,GT,GTT,GTTT,GTTTTT,GTTTTTT,GTTTTTTT), RS1001212789 (2:99249353 G>A), RS1001243727 (2:99248943 A>G), RS1001440499 (2:99255164 A>G), RS1001609280 (2:99262891 C>A,T), RS1001639876 (2:99255446 C>A), RS1002168000 (2:99261036 G>T)

Disease associations

OMIM: gene MIM:616547 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001241_13	Bipolar disorder	3.000000e-06
GCST90002385_137	High light scatter reticulocyte count	1.000000e-09
GCST90002386_253	High light scatter reticulocyte percentage of red cells	7.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007986	reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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