LYG1

Summary

LYG1 (lysozyme g1, HGNC:27014) is a protein-coding gene on chromosome 2q11.2, encoding Lysozyme g-like protein 1 (Q8N1E2).

Predicted to enable lysozyme activity. Predicted to be involved in defense response to Gram-positive bacterium. Predicted to be active in extracellular region.

Source: NCBI Gene 129530 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 29 total
• MANE Select transcript: NM_174898

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27014
Approved symbol	LYG1
Name	lysozyme g1
Location	2q11.2
Locus type	gene with protein product
Status	Approved
Aliases	SALW1939, LYGA1
Ensembl gene	ENSG00000144214
Ensembl biotype	protein_coding
OMIM	621066
Entrez	129530

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000308528, ENST00000409448, ENST00000905974, ENST00000905975, ENST00000905976, ENST00000946652, ENST00000946653, ENST00000946654

RefSeq mRNA: 2 — MANE Select: NM_174898 NM_001371380, NM_174898

CCDS: CCDS2043

Canonical transcript exons

ENST00000308528 — 7 exons

Exon	Start	End
ENSE00001072059	99284688	99284820
ENSE00001072063	99291237	99291421
ENSE00001164349	99298459	99298549
ENSE00001199852	99295628	99295702
ENSE00001199860	99301050	99301197
ENSE00001199878	99292536	99292640
ENSE00001222196	99284238	99284511

Expression profiles

Bgee: expression breadth ubiquitous, 165 present calls, max score 85.62.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0011 / max 1.7022, expressed in 1 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
29880	0.0011	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	85.62	silver quality
adult mammalian kidney	UBERON:0000082	85.25	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.90	gold quality
metanephros cortex	UBERON:0010533	81.14	gold quality
kidney	UBERON:0002113	78.39	gold quality
granulocyte	CL:0000094	77.32	gold quality
pancreatic ductal cell	CL:0002079	76.05	silver quality
right lobe of liver	UBERON:0001114	75.82	gold quality
ileal mucosa	UBERON:0000331	73.70	silver quality
cortex of kidney	UBERON:0001225	73.67	gold quality
cerebellar hemisphere	UBERON:0002245	72.89	gold quality
cerebellar cortex	UBERON:0002129	72.74	gold quality
lower esophagus mucosa	UBERON:0035834	71.93	gold quality
mucosa of transverse colon	UBERON:0004991	71.88	gold quality
right hemisphere of cerebellum	UBERON:0014890	71.67	gold quality
cerebellum	UBERON:0002037	71.33	gold quality
spleen	UBERON:0002106	71.09	gold quality
right testis	UBERON:0004534	71.00	gold quality
oocyte	CL:0000023	70.69	gold quality
tibialis anterior	UBERON:0001385	70.68	silver quality
apex of heart	UBERON:0002098	70.45	gold quality
gastrocnemius	UBERON:0001388	70.21	gold quality
body of uterus	UBERON:0009853	70.19	gold quality
left ventricle myocardium	UBERON:0006566	69.94	gold quality
left testis	UBERON:0004533	69.83	gold quality
cardiac muscle of right atrium	UBERON:0003379	69.72	gold quality
muscle of leg	UBERON:0001383	69.17	gold quality
metanephros	UBERON:0000081	69.13	gold quality
endocervix	UBERON:0000458	68.89	gold quality
ectocervix	UBERON:0012249	68.70	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting LYG1, 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-6875-3P	99.82	70.26	2983
HSA-MIR-485-5P	99.10	64.78	1889
HSA-MIR-6884-5P	99.10	64.50	1987
HSA-MIR-8070	99.07	69.30	1303
HSA-MIR-8066	99.05	68.66	1532
HSA-MIR-1304-5P	98.90	68.58	1054

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lygl1	ENSDARG00000056874
danio_rerio	zgc:162941	ENSDARG00000071701
danio_rerio	lygl2	ENSDARG00000099562
mus_musculus	Lyg1	ENSMUSG00000026085
rattus_norvegicus	Lyg1	ENSRNOG00000047233

Paralogs (1): LYG2 (ENSG00000185674)

Protein

Protein identifiers

Lysozyme g-like protein 1 — Q8N1E2 (reviewed: Q8N1E2)

All UniProt accessions (1): Q8N1E2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the glycosyl hydrolase 23 family.

RefSeq proteins (2): NP_001358309, NP_777558* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002152	Glyco_hydro_23	Family
IPR023346	Lysozyme-like_dom_sf	Homologous_superfamily

UniProt features (4 total): disulfide bond 2, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N1E2-F1	82.65	0.66

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 (2): 24–80, 38–49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 32 (showing top): GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, 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, DURCHDEWALD_SKIN_CARCINOGENESIS_DN, GOMF_LYSOZYME_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_GLYCOSYL_BONDS, GOBP_RESPONSE_TO_BACTERIUM, chr2q11, GOMF_HYDROLASE_ACTIVITY_HYDROLYZING_O_GLYCOSYL_COMPOUNDS, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, FORTSCHEGGER_PHF8_TARGETS_UP

GO Biological Process (2): peptidoglycan catabolic process (GO:0009253), 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 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

268 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LYG1	IFT70A	Q86WT1	578
LYG1	EPM2AIP1	Q7L775	571
LYG1	RTF2	Q9BY42	542
LYG1	SHROOM4	Q9ULL8	507
LYG1	ZSWIM3	Q96MP5	506
LYG1	HENMT1	Q5T8I9	479
LYG1	SMAP1	Q8IYB5	478
LYG1	DDX27	Q96GQ7	474
LYG1	ZMYND12	Q9H0C1	449
LYG1	RPL22L1	Q6P5R6	448
LYG1	SNX24	Q9Y343	442
LYG1	RNLS	Q5VYX0	433
LYG1	ERP27	Q96DN0	415
LYG1	TSPYL5	Q86VY4	402
LYG1	SLC16A5	O15375	402

IntAct

11 interactions, top by confidence:

A	B	Type	Score
VENTX	LYG1	psi-mi:“MI:0915”(physical association)	0.560
TMEM179B	LYG1	psi-mi:“MI:0915”(physical association)	0.560
HTT	LYG1	psi-mi:“MI:0915”(physical association)	0.560
LYG1	ENY2	psi-mi:“MI:0915”(physical association)	0.400
VENTX	LYG1	psi-mi:“MI:0915”(physical association)	0.000
LYG1	TMEM179B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (4): VENTX (Two-hybrid), TMEM179B (Two-hybrid), ENY2 (Proximity Label-MS), LYG1 (Affinity Capture-RNA)

ESM2 similar proteins: C1IIX1, G3XDD8, G3XDT7, O02119, P00698, P00701, P00702, P00703, P00704, P00705, P00706, P00707, P00717, P00718, P00719, P05105, P11941, P12068, P17897, P27042, P37161, P48816, P49663, P50717, P50718, P51782, P61133, P61944, P82174, P84492, P85045, P86383, Q05820, Q29RT1, Q3V1I0, Q6L6Q5, Q6L6Q6, Q7LZQ2, Q7LZQ3, Q7LZR3

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1295 predictions. Top by Δscore:

Variant	Effect	Δscore
2:99284511:CCTG:C	acceptor_loss	0.9900
2:99284512:CT:C	acceptor_loss	0.9900
2:99284683:CGTA:C	donor_loss	0.9900
2:99284684:GTAC:G	donor_loss	0.9900
2:99284685:TA:T	donor_loss	0.9900
2:99284687:C:CG	donor_loss	0.9900
2:99284687:CCT:C	donor_gain	0.9900
2:99284819:TCC:T	acceptor_loss	0.9900
2:99284821:C:CC	acceptor_gain	0.9900
2:99284821:CTG:C	acceptor_loss	0.9900
2:99284822:T:A	acceptor_loss	0.9900
2:99295621:CACT:C	donor_loss	0.9900
2:99295622:ACTC:A	donor_loss	0.9900
2:99295623:CTCA:C	donor_loss	0.9900
2:99295624:T:TC	donor_loss	0.9900
2:99295625:C:CC	donor_loss	0.9900
2:99295626:AC:A	donor_gain	0.9900
2:99295627:CC:C	donor_gain	0.9900
2:99295701:CA:C	acceptor_gain	0.9900
2:99295701:CACT:C	acceptor_gain	0.9900
2:99295704:T:C	acceptor_gain	0.9900
2:99284508:CCAC:C	acceptor_gain	0.9800
2:99284509:CAC:C	acceptor_gain	0.9800
2:99284509:CACC:C	acceptor_gain	0.9800
2:99284512:C:CC	acceptor_gain	0.9800
2:99284687:CCTCT:C	donor_gain	0.9800
2:99284816:GGGTC:G	acceptor_gain	0.9800
2:99284819:TC:T	acceptor_gain	0.9800
2:99284820:CC:C	acceptor_gain	0.9800
2:99291293:T:TA	donor_gain	0.9800

AlphaMissense

1266 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:99284396:G:C	F194L	0.975
2:99284396:G:T	F194L	0.975
2:99284398:A:G	F194L	0.975
2:99284719:A:C	F145L	0.962
2:99284719:A:T	F145L	0.962
2:99284721:A:G	F145L	0.962
2:99284422:C:G	A186P	0.957
2:99284397:A:G	F194S	0.950
2:99284424:C:G	R185P	0.940
2:99284397:A:C	F194C	0.921
2:99291409:G:A	S54F	0.920
2:99284421:G:T	A186D	0.916
2:99284441:G:C	C179W	0.911
2:99284712:A:G	W148R	0.908
2:99284712:A:T	W148R	0.908
2:99284442:C:T	C179Y	0.902
2:99284444:G:C	F178L	0.901
2:99284444:G:T	F178L	0.901
2:99284446:A:G	F178L	0.901
2:99284501:A:C	C159W	0.901
2:99284436:T:A	D181V	0.891
2:99291307:C:T	G88D	0.887
2:99284502:C:G	C159S	0.886
2:99284503:A:T	C159S	0.886
2:99284412:A:G	L189P	0.884
2:99284502:C:T	C159Y	0.884
2:99284443:A:G	C179R	0.880
2:99284437:C:G	D181H	0.878
2:99284505:A:T	L158H	0.878
2:99284503:A:G	C159R	0.877

dbSNP variants (sampled 300 via entrez): RS1000061047 (2:99301432 AGAGT>A), RS1000305563 (2:99294145 C>G,T), RS1000873347 (2:99287110 G>A), RS1001108874 (2:99293480 C>T), RS1001131638 (2:99287272 GA>G), RS1001231510 (2:99301230 C>A,T), RS1001311243 (2:99294367 A>G), RS1001325343 (2:99287456 C>G), RS1001593371 (2:99292935 T>C,G), RS1002466789 (2:99293546 T>G), RS1002643612 (2:99285060 A>G), RS1002839589 (2:99287838 T>C), RS1002907286 (2:99299484 T>C), RS1002957685 (2:99299246 C>A,T), RS1003132633 (2:99290661 G>A)

Disease associations

OMIM: gene MIM:621066 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001241_13	Bipolar disorder	3.000000e-06
GCST90000514_34	Gastroesophageal reflux disease	3.000000e-11

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
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	decreases expression	1
bisphenol S	affects cotreatment, decreases expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	increases methylation	1
Asbestos, Crocidolite	increases methylation	1
Acrylamide	increases expression	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

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