LYZL1

Summary

LYZL1 (lysozyme like 1, HGNC:30502) is a protein-coding gene on chromosome 10p12.1-p11.23, encoding Lysozyme-like protein 1 (Q6UWQ5).

Predicted to enable lysozyme activity. Predicted to be located in extracellular region.

Source: NCBI Gene 84569 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 39 total
• MANE Select transcript: NM_032517

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30502
Approved symbol	LYZL1
Name	lysozyme like 1
Location	10p12.1-p11.23
Locus type	gene with protein product
Status	Approved
Aliases	MGC33408, LYC2
Ensembl gene	ENSG00000120563
Ensembl biotype	protein_coding
Entrez	84569

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 nonsense_mediated_decay

ENST00000375500, ENST00000494304, ENST00000649382

RefSeq mRNA: 1 — MANE Select: NM_032517 NM_032517

CCDS: CCDS31174

Canonical transcript exons

ENST00000649382 — 5 exons

Exon	Start	End
ENSE00001904929	29310990	29311232
ENSE00002433099	29292519	29292677
ENSE00002455390	29310110	29310188
ENSE00003837820	29289070	29289230
ENSE00003839264	29291843	29292006

Expression profiles

Bgee: expression breadth broad, 35 present calls, max score 94.44.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0570 / max 64.0541, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
104515	0.0484	3
205800	0.0086	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.44	gold quality
left testis	UBERON:0004533	92.43	gold quality
right testis	UBERON:0004534	92.07	gold quality
testis	UBERON:0000473	88.81	gold quality
sperm	CL:0000019	84.81	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	69.05	gold quality
epithelial cell of pancreas	CL:0000083	68.31	gold quality
tibialis anterior	UBERON:0001385	56.38	silver quality
right uterine tube	UBERON:0001302	55.02	gold quality
right lobe of liver	UBERON:0001114	54.48	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
pancreatic ductal cell	CL:0002079	51.50	silver quality
myocardium	UBERON:0002349	50.25	gold quality
deltoid	UBERON:0001476	50.15	gold quality
lower lobe of lung	UBERON:0008949	48.79	silver quality
ileal mucosa	UBERON:0000331	47.76	silver quality
nasal cavity epithelium	UBERON:0005384	47.45	gold quality
buccal mucosa cell	CL:0002336	46.73	gold quality
quadriceps femoris	UBERON:0001377	46.71	gold quality
liver	UBERON:0002107	46.20	gold quality
vastus lateralis	UBERON:0001379	45.49	gold quality
adult organism	UBERON:0007023	45.22	gold quality
layer of synovial tissue	UBERON:0007616	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
endocervix	UBERON:0000458	42.50	gold quality
skeletal muscle tissue	UBERON:0001134	41.47	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.61

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting LYZL1, 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-548N	99.98	71.94	4170
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-3617-5P	99.75	69.41	1968
HSA-MIR-641	99.75	69.35	1975
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-642A-5P	99.51	65.10	1152
HSA-MIR-5695	99.41	67.48	1047
HSA-MIR-4520-2-3P	99.14	69.28	1009
HSA-MIR-1253	99.12	67.08	1688
HSA-MIR-6770-5P	98.97	66.76	1853

Cross-species orthologs

14 orthologs

Organism	Symbol	Gene ID
danio_rerio	lyz	ENSDARG00000057789
mus_musculus	Lyzl1	ENSMUSG00000024233
rattus_norvegicus	Lyzl1	ENSRNOG00000016295
drosophila_melanogaster	LysB	FBGN0004425
drosophila_melanogaster	LysD	FBGN0004427
drosophila_melanogaster	LysE	FBGN0004428
drosophila_melanogaster	LysP	FBGN0004429
drosophila_melanogaster	LysS	FBGN0004430
drosophila_melanogaster	LysX	FBGN0004431
drosophila_melanogaster	CG16756	FBGN0029765
drosophila_melanogaster	CG7798	FBGN0034092
drosophila_melanogaster	CG16799	FBGN0034538
drosophila_melanogaster	CG11159	FBGN0034539
drosophila_melanogaster	CG30062	FBGN0050062

Paralogs (8): LYZ (ENSG00000090382), SPACA3 (ENSG00000141316), LYZL2 (ENSG00000151033), LYZL4 (ENSG00000157093), LALBA (ENSG00000167531), SPACA5B (ENSG00000171478), SPACA5 (ENSG00000171489), LYZL6 (ENSG00000275722)

Protein

Protein identifiers

Lysozyme-like protein 1 — Q6UWQ5 (reviewed: Q6UWQ5)

All UniProt accessions (3): A0A080YUZ8, Q6UWQ5, H0YDZ2

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Monomer.

Subcellular location. Secreted.

Similarity. Belongs to the glycosyl hydrolase 22 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6UWQ5-1	1	yes
Q6UWQ5-2	2

RefSeq proteins (1): NP_115906* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000974	Glyco_hydro_22_lys	Family
IPR001916	Glyco_hydro_22	Family
IPR019799	Glyco_hydro_22_CS	Domain
IPR023346	Lysozyme-like_dom_sf	Homologous_superfamily

Pfam: PF00062

UniProt features (13 total): disulfide bond 4, active site 2, signal peptide 1, chain 1, splice variant 1, sequence variant 1, sequence conflict 1, domain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UWQ5-F1	92.44	0.84

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 (2): 54; 71

Disulfide bonds (4): 25–145, 49–133, 83–98, 94–112

Glycosylation sites (1): 58

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 29 (showing top): chr10p12, GOMF_LYSOZYME_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_GLYCOSYL_BONDS, GOMF_HYDROLASE_ACTIVITY_HYDROLYZING_O_GLYCOSYL_COMPOUNDS, GOMF_PEPTIDOGLYCAN_MURALYTIC_ACTIVITY, GSE14415_NATURAL_TREG_VS_FOXP3_KO_NATURAL_TREG_DN, MIR4694_3P, MIR6780A_5P, MIR1273H_5P, MIR6770_5P, MIR6779_5P, MIR30B_3P, MIR3689A_3P_MIR3689B_3P_MIR3689C, MIR5695, MIR6892_3P

GO Biological Process (0):

GO Molecular Function (3): lysozyme activity (GO:0003796), 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
hydrolase activity, hydrolyzing O-glycosyl compounds	1
peptidoglycan muralytic activity	1
catalytic activity	1
hydrolase activity	1
cellular anatomical structure	1

Protein interactions and networks

STRING

584 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LYZL1	MPO	P05164	853
LYZL1	PRTN3	P15637	849
LYZL1	CTSG	P08311	826
LYZL1	LCN1	P31025	787
LYZL1	LTF	P02788	763
LYZL1	SDF4	Q9BRK5	721
LYZL1	PIP	P12273	663
LYZL1	ELANE	P08246	662
LYZL1	DCD	P58461	625
LYZL1	LACRT	Q9GZZ8	621
LYZL1	S100A9	P06702	596
LYZL1	DMBT1	Q9UGM3	591
LYZL1	AMY1B	P04745	556
LYZL1	PIGR	P01833	554
LYZL1	SCGB1D1	O95968	544

IntAct

5 interactions, top by confidence:

A	B	Type	Score
GKN1	CST4	psi-mi:“MI:0914”(association)	0.530
LYZL1	XAGE3	psi-mi:“MI:0915”(physical association)	0.400
LYZL1	ZZEF1	psi-mi:“MI:0914”(association)	0.350
LYZL1	MAN2B1	psi-mi:“MI:0914”(association)	0.350

BioGRID (143): FAM198A (Affinity Capture-MS), LYZL1 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), EDEM1 (Affinity Capture-MS), STS (Affinity Capture-MS), EOGT (Affinity Capture-MS), ZZEF1 (Affinity Capture-MS), GALNS (Affinity Capture-MS), FIGNL1 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), ARSK (Affinity Capture-MS), TMEM131 (Affinity Capture-MS), GALNT18 (Affinity Capture-MS), POGLUT1 (Affinity Capture-MS)

ESM2 similar proteins: A0JNM6, C5H5C4, O70309, P04421, P12068, P12069, P16973, P17607, P18084, P26012, P26013, P30201, P61626, P61627, P61628, P61629, P61630, P61631, P61632, P61633, P61634, P67977, P67978, P67979, P67980, P79158, P79179, P79180, P79239, P79268, P79294, P79687, P79806, P79811, P79847, P80189, P80190, P80747, Q06283, Q06284

Diamond homologs: A0JNM6, A2AE20, A6QQ77, B6VH75, B6VH76, G3XDT7, O75951, P00697, P00698, P00699, P00700, P00701, P00702, P00703, P00704, P00705, P00706, P00707, P00708, P04421, P08905, P11375, P11376, P11941, P12066, P12067, P12068, P12069, P16973, P17607, P17897, P19849, P22910, P24364, P24533, P30201, P37712, P37713, P49663, P61626

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	4
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

562 predictions. Top by Δscore:

Variant	Effect	Δscore
10:29289231:G:GG	donor_gain	1.0000
10:29310104:TTACA:T	acceptor_loss	1.0000
10:29310106:ACAG:A	acceptor_loss	1.0000
10:29310107:CA:C	acceptor_loss	1.0000
10:29310108:A:AG	acceptor_gain	1.0000
10:29310108:A:C	acceptor_loss	1.0000
10:29310109:G:GG	acceptor_gain	1.0000
10:29310109:GCCTT:G	acceptor_gain	1.0000
10:29289189:G:GT	donor_gain	0.9900
10:29289216:G:GT	donor_gain	0.9900
10:29289281:G:GT	donor_gain	0.9900
10:29292007:G:GG	donor_gain	0.9900
10:29292513:CTCCA:C	acceptor_loss	0.9900
10:29292514:TCCA:T	acceptor_loss	0.9900
10:29292515:CCAG:C	acceptor_loss	0.9900
10:29292516:CAGG:C	acceptor_loss	0.9900
10:29292517:A:AG	acceptor_gain	0.9900
10:29292517:A:T	acceptor_loss	0.9900
10:29292517:AG:A	acceptor_gain	0.9900
10:29292517:AGG:A	acceptor_gain	0.9900
10:29292518:G:GG	acceptor_gain	0.9900
10:29292518:GG:G	acceptor_gain	0.9900
10:29292518:GGG:G	acceptor_gain	0.9900
10:29292518:GGGAT:G	acceptor_gain	0.9900
10:29292673:CTCAG:C	donor_loss	0.9900
10:29292674:TCAGG:T	donor_loss	0.9900
10:29292675:CAGG:C	donor_loss	0.9900
10:29292676:AG:A	donor_loss	0.9900
10:29292677:GG:G	donor_loss	0.9900
10:29292678:GT:G	donor_loss	0.9900

AlphaMissense

979 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:29310999:G:C	W129C	0.994
10:29310999:G:T	W129C	0.994
10:29311035:G:C	W141C	0.992
10:29311035:G:T	W141C	0.992
10:29310990:G:C	W126C	0.991
10:29310990:G:T	W126C	0.991
10:29311009:T:A	C133S	0.986
10:29311010:G:C	C133S	0.986
10:29292520:G:C	W47C	0.985
10:29292520:G:T	W47C	0.985
10:29310997:T:A	W129R	0.985
10:29310997:T:C	W129R	0.985
10:29292597:G:T	G73V	0.984
10:29310113:T:C	L101S	0.984
10:29292626:T:A	C83S	0.983
10:29292627:G:C	C83S	0.983
10:29292659:T:A	C94S	0.983
10:29292660:G:C	C94S	0.983
10:29292596:G:T	G73C	0.982
10:29310145:T:A	C112S	0.982
10:29310146:G:C	C112S	0.982
10:29310149:C:A	A113D	0.981
10:29292006:T:A	W47R	0.980
10:29292006:T:C	W47R	0.980
10:29292600:T:C	I74T	0.979
10:29292603:T:C	F75S	0.978
10:29292603:T:G	F75C	0.978
10:29292609:T:C	I77T	0.978
10:29310146:G:A	C112Y	0.978
10:29311010:G:A	C133Y	0.978

dbSNP variants (sampled 300 via entrez): RS1000206016 (10:29293469 G>A), RS1000261857 (10:29315483 C>T), RS1000273778 (10:29317240 G>A), RS1000316099 (10:29315302 G>A), RS1000341984 (10:29297577 A>G), RS1000415316 (10:29301125 C>A), RS1000447530 (10:29303489 C>A,T), RS1000490112 (10:29312143 T>C), RS1000750704 (10:29311172 A>C), RS1000787895 (10:29295740 C>G), RS1000855773 (10:29303314 T>A), RS1000872 (10:29315727 T>C), RS1001398148 (10:29289715 G>A), RS1001459352 (10:29314777 T>C,G), RS1001681381 (10:29299993 C>T)

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

7 associations (top):

Study	Trait	p-value
GCST001841_9	Palmitoleic acid (16:1n-7) levels	2.000000e-06
GCST003486_7	Response to fenofibrate (LDL cholesterol levels)	9.000000e-06
GCST003855_7	Gut microbiota (bacterial taxa)	6.000000e-09
GCST003855_8	Gut microbiota (bacterial taxa)	1.000000e-08
GCST009391_231	Metabolite levels	4.000000e-06
GCST009544_2	Cleft lip with or without cleft palate x maternal periconceptional smoking interaction (parent of origin effect)	2.000000e-06
GCST90020028_37	Hip circumference adjusted for BMI	5.000000e-09

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0007804	LDL cholesterol change measurement
EFO:0007874	gut microbiome measurement
EFO:0010493	glycodeoxycholate measurement
EFO:0003959	cleft lip
EFO:0005939	parental genotype effect measurement
EFO:0009115	tobacco smoke exposure measurement
EFO:0008039	BMI-adjusted hip circumference

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
2,3,4,5-tetrachlorophenate	affects response to substance	1
CGP 52608	affects binding, increases reaction	1
Benzo(a)pyrene	affects methylation	1

Clinical trials (associated diseases)

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