LYZL2

Summary

LYZL2 (lysozyme like 2, HGNC:29613) is a protein-coding gene on chromosome 10p11.23, encoding Lysozyme-like protein 2 (Q7Z4W2).

Lysozymes (see LYZ; MIM 153450), especially C-type lysozymes, are well-recognized bacteriolytic factors widely distributed in the animal kingdom and play a mainly protective role in host defense. LYZL2 is a member of a family of lysozyme-like genes (Zhang et al., 2005 [PubMed 16014814]).

Source: NCBI Gene 119180 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 42 total
• MANE Select transcript: NM_183058

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29613
Approved symbol	LYZL2
Name	lysozyme like 2
Location	10p11.23
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000151033
Ensembl biotype	protein_coding
OMIM	612748
Entrez	119180

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000375318, ENST00000647634

RefSeq mRNA: 1 — MANE Select: NM_183058 NM_183058

CCDS: CCDS7167

Canonical transcript exons

ENST00000647634 — 5 exons

Exon	Start	End
ENSE00001840640	30611779	30612024
ENSE00002507068	30612822	30612900
ENSE00002535784	30626105	30626263
ENSE00003831839	30629593	30629753
ENSE00003831860	30626777	30626940

Expression profiles

Bgee: expression breadth broad, 19 present calls, max score 94.10.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0342 / max 34.2825, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
108946	0.0342	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	94.10	gold quality
right testis	UBERON:0004534	94.00	gold quality
testis	UBERON:0000473	93.60	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.12	gold quality
adrenal tissue	UBERON:0018303	38.02	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
right uterine tube	UBERON:0001302	36.72	silver quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
liver	UBERON:0002107	31.53	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
right lobe of liver	UBERON:0001114	29.27	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
right adrenal gland cortex	UBERON:0035827	28.77	gold quality
cortex of kidney	UBERON:0001225	28.66	gold quality
duodenum	UBERON:0002114	28.14	gold quality
right coronary artery	UBERON:0001625	28.10	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	27.72	gold quality
lymph node	UBERON:0000029	27.57	gold quality
muscle of leg	UBERON:0001383	27.34	gold quality
metanephros cortex	UBERON:0010533	27.28	gold quality
tonsil	UBERON:0002372	27.05	gold quality
gastrocnemius	UBERON:0001388	26.56	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting LYZL2, 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

Literature-anchored findings (GeneRIF, showing 1)

• We identified a significant genetic association between dental caries of the anterior mandibular teeth and LYZL2 (p value = 9e-9), which codes a bacteriolytic agent thought to be involved in host defense. (PMID:23064961)

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), LYZL1 (ENSG00000120563), SPACA3 (ENSG00000141316), LYZL4 (ENSG00000157093), LALBA (ENSG00000167531), SPACA5B (ENSG00000171478), SPACA5 (ENSG00000171489), LYZL6 (ENSG00000275722)

Protein

Protein identifiers

Lysozyme-like protein 2 — Q7Z4W2 (reviewed: Q7Z4W2)

All UniProt accessions (2): Q7Z4W2, A0A080YUZ9

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Monomer.

Subcellular location. Secreted.

Tissue specificity. Expressed in testis, epididymis and placenta.

Similarity. Belongs to the glycosyl hydrolase 22 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q7Z4W2-1	1	yes
Q7Z4W2-2	2

RefSeq proteins (1): NP_898881* (*=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 (12 total): disulfide bond 4, active site 2, signal peptide 1, chain 1, splice variant 1, sequence variant 1, domain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z4W2-F1	92.77	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: 18 (showing top): BROWN_MYELOID_CELL_DEVELOPMENT_UP, GOMF_LYSOZYME_ACTIVITY, chr10p11, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_GLYCOSYL_BONDS, GOMF_HYDROLASE_ACTIVITY_HYDROLYZING_O_GLYCOSYL_COMPOUNDS, CHYLA_CBFA2T3_TARGETS_UP, GOMF_PEPTIDOGLYCAN_MURALYTIC_ACTIVITY, MIR4694_3P, MIR6780A_5P, MIR1273H_5P, MIR6770_5P, MIR6779_5P, MIR30B_3P, MIR3689A_3P_MIR3689B_3P_MIR3689C, MIR5695

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

360 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LYZL2	C20orf173	Q96LM9	507
LYZL2	PGLYRP1	O75594	449
LYZL2	AJAP1	Q9UKB5	447
LYZL2	SPATA31G1	Q5VYM1	445
LYZL2	LYG2	Q86SG7	411
LYZL2	CABS1	Q96KC9	400
LYZL2	TMCO5A	Q8N6Q1	396
LYZL2	CXorf65	A6NEN9	370
LYZL2	CCDC187	A0A096LP49	368
LYZL2	TMCO2	Q7Z6W1	359
LYZL2	RIMBP3	Q9UFD9	354
LYZL2	CCDC54	Q8NEL0	348
LYZL2	ZC3H11D	Q8NA57	348
LYZL2	FAM209A	Q5JX71	348
LYZL2	CFAP184	Q2M329	325
LYZL2	CIMIP4	O43247	325

IntAct

3 interactions, top by confidence:

A	B	Type	Score
LYZL2	ZZEF1	psi-mi:“MI:0914”(association)	0.350
LYZL2	POTEF	psi-mi:“MI:0914”(association)	0.350

BioGRID (126): GALNT18 (Affinity Capture-MS), ENTPD5 (Affinity Capture-MS), LOXL2 (Affinity Capture-MS), B4GALNT4 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), FKBP14 (Affinity Capture-MS), SULF1 (Affinity Capture-MS), VWDE (Affinity Capture-MS), PCYOX1L (Affinity Capture-MS), TMEM67 (Affinity Capture-MS), FIGNL1 (Affinity Capture-MS), GAS6 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), EDEM1 (Affinity Capture-MS), ERO1LB (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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	35
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

525 predictions. Top by Δscore:

Variant	Effect	Δscore
10:30612815:CTCTT:C	donor_loss	1.0000
10:30612816:TCTTA:T	donor_loss	1.0000
10:30612817:CTTA:C	donor_loss	1.0000
10:30612818:TTA:T	donor_loss	1.0000
10:30612819:T:TG	donor_loss	1.0000
10:30612820:A:AC	donor_gain	1.0000
10:30612820:ACCA:A	donor_loss	1.0000
10:30612821:C:CC	donor_gain	1.0000
10:30612821:C:CG	donor_loss	1.0000
10:30612896:CAAGG:C	acceptor_gain	1.0000
10:30612901:C:CC	acceptor_gain	1.0000
10:30629525:T:TA	donor_gain	1.0000
10:30629591:A:AC	donor_gain	1.0000
10:30629592:C:CC	donor_gain	1.0000
10:30612897:AAGG:A	acceptor_gain	0.9900
10:30612897:AAGGC:A	acceptor_loss	0.9900
10:30612898:AGG:A	acceptor_gain	0.9900
10:30612899:GG:G	acceptor_gain	0.9900
10:30612899:GGC:G	acceptor_loss	0.9900
10:30612900:GCT:G	acceptor_loss	0.9900
10:30612901:C:G	acceptor_loss	0.9900
10:30612902:T:G	acceptor_loss	0.9900
10:30626099:CCTCA:C	donor_loss	0.9900
10:30626260:ATCCC:A	acceptor_loss	0.9900
10:30626261:TCC:T	acceptor_gain	0.9900
10:30626262:CC:C	acceptor_gain	0.9900
10:30626262:CCC:C	acceptor_gain	0.9900
10:30626263:CC:C	acceptor_gain	0.9900
10:30626264:C:CC	acceptor_gain	0.9900
10:30626264:CT:C	acceptor_loss	0.9900

AlphaMissense

981 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:30612015:C:A	W129C	0.988
10:30612015:C:G	W129C	0.988
10:30612024:C:A	W126C	0.982
10:30612024:C:G	W126C	0.982
10:30612004:C:G	C133S	0.975
10:30612005:A:T	C133S	0.975
10:30611979:C:A	W141C	0.972
10:30611979:C:G	W141C	0.972
10:30626122:C:G	C94S	0.971
10:30626123:A:T	C94S	0.971
10:30626262:C:A	W47C	0.971
10:30626262:C:G	W47C	0.971
10:30612017:A:G	W129R	0.970
10:30612017:A:T	W129R	0.970
10:30612864:C:G	C112S	0.969
10:30612865:A:T	C112S	0.969
10:30626155:C:G	C83S	0.969
10:30626156:A:T	C83S	0.969
10:30626179:A:C	F75C	0.968
10:30612861:G:T	A113D	0.964
10:30626179:A:G	F75S	0.961
10:30626238:G:C	S55R	0.961
10:30626238:G:T	S55R	0.961
10:30626240:T:G	S55R	0.961
10:30626257:C:G	C49S	0.961
10:30626258:A:T	C49S	0.961
10:30626166:G:C	S79R	0.960
10:30626166:G:T	S79R	0.960
10:30626168:T:G	S79R	0.960
10:30626178:G:C	F75L	0.960

dbSNP variants (sampled 300 via entrez): RS1000006710 (10:30627276 C>G), RS1000052806 (10:30605915 A>T), RS1000117739 (10:30621556 GTGT>G), RS1000171916 (10:30624714 G>A,T), RS1000272050 (10:30621249 T>C), RS1000672299 (10:30627467 T>C), RS1000887415 (10:30630769 G>A), RS1001052769 (10:30617699 G>A,C,T), RS1001069047 (10:30607173 A>G), RS1001082677 (10:30630995 C>A), RS1001150335 (10:30605994 G>C,T), RS1001275062 (10:30620323 G>A), RS1001413867 (10:30626033 T>C), RS1001413889 (10:30620658 T>A), RS1001514663 (10:30619790 C>T)

Disease associations

OMIM: gene MIM:612748 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): breast ductal adenocarcinoma (MONDO:0005590)

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001713_9	Dental caries	9.000000e-09
GCST003381_3	Bone mineral density (femoral neck)	7.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007785	femoral neck bone mineral density

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D018270	Carcinoma, Ductal, Breast	C04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390

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
bisphenol A	increases expression	1
Aflatoxin B1	increases methylation	1
Zinc Sulfate	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03414970	PHASE3	ACTIVE_NOT_RECRUITING	Hypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344	PHASE2	TERMINATED	Docetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999	PHASE2	NOT_YET_RECRUITING	Randomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364	PHASE1/PHASE2	SUSPENDED	High Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855	PHASE1/PHASE2	COMPLETED	Talimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908	EARLY_PHASE1	COMPLETED	Broccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041	EARLY_PHASE1	COMPLETED	Intraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974	Not specified	ACTIVE_NOT_RECRUITING	Nipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198	Not specified	TERMINATED	Oncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397	Not specified	UNKNOWN	MRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532	Not specified	COMPLETED	Living Well After Breast Surgery