LYSMD3

Summary

LYSMD3 (LysM domain containing 3, HGNC:26969) is a protein-coding gene on chromosome 5q14.3, encoding LysM and putative peptidoglycan-binding domain-containing protein 3 (Q7Z3D4). Essential for Golgi structural integrity.

Enables peptidoglycan binding activity. Involved in Golgi organization. Located in Golgi membrane and plasma membrane.

Source: NCBI Gene 116068 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 42 total
• MANE Select transcript: NM_198273

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26969
Approved symbol	LYSMD3
Name	LysM domain containing 3
Location	5q14.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13542
Ensembl gene	ENSG00000176018
Ensembl biotype	protein_coding
Entrez	116068

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 nonsense_mediated_decay

ENST00000315948, ENST00000453259, ENST00000500869, ENST00000509384, ENST00000873901, ENST00000873902, ENST00000913812

RefSeq mRNA: 2 — MANE Select: NM_198273 NM_001286812, NM_198273

CCDS: CCDS43338, CCDS68911

Canonical transcript exons

ENST00000315948 — 3 exons

Exon	Start	End
ENSE00002290750	90515626	90519484
ENSE00003504698	90529448	90529584
ENSE00003687345	90525035	90525300

Expression profiles

Bgee: expression breadth ubiquitous, 242 present calls, max score 92.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.6838 / max 1034.5309, expressed in 1774 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
62528	15.3806	1770
62529	0.3032	125

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
parietal pleura	UBERON:0002400	92.53	gold quality
mucosa of paranasal sinus	UBERON:0005030	92.42	gold quality
visceral pleura	UBERON:0002401	92.29	gold quality
epithelial cell of pancreas	CL:0000083	91.64	gold quality
palpebral conjunctiva	UBERON:0001812	91.47	gold quality
lower lobe of lung	UBERON:0008949	91.43	gold quality
calcaneal tendon	UBERON:0003701	90.96	gold quality
eye	UBERON:0000970	90.82	gold quality
germinal epithelium of ovary	UBERON:0001304	90.61	gold quality
ileal mucosa	UBERON:0000331	89.98	gold quality
mucosa of sigmoid colon	UBERON:0004993	89.66	gold quality
tibia	UBERON:0000979	89.64	gold quality
endometrium	UBERON:0001295	89.64	gold quality
jejunal mucosa	UBERON:0000399	89.34	gold quality
colonic mucosa	UBERON:0000317	89.19	gold quality
islet of Langerhans	UBERON:0000006	88.91	gold quality
pigmented layer of retina	UBERON:0001782	88.91	gold quality
superficial temporal artery	UBERON:0001614	88.84	gold quality
kidney epithelium	UBERON:0004819	88.68	silver quality
colonic epithelium	UBERON:0000397	88.56	gold quality
placenta	UBERON:0001987	88.16	gold quality
seminal vesicle	UBERON:0000998	87.42	gold quality
epithelium of nasopharynx	UBERON:0001951	87.26	gold quality
cauda epididymis	UBERON:0004360	86.71	gold quality
cartilage tissue	UBERON:0002418	86.64	gold quality
duodenum	UBERON:0002114	86.61	gold quality
layer of synovial tissue	UBERON:0007616	86.53	gold quality
epithelium of mammary gland	UBERON:0003244	86.25	gold quality
mammary duct	UBERON:0001765	86.19	gold quality
esophagus squamous epithelium	UBERON:0006920	86.14	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

170 targeting LYSMD3, 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-3163	100.00	77.23	8605
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-607	99.97	73.62	5593

Literature-anchored findings (GeneRIF, showing 1)

• LYSMD3: A mammalian pattern recognition receptor for chitin. (PMID:34289364)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lysmd3	ENSDARG00000024693
mus_musculus	Lysmd3	ENSMUSG00000035840
rattus_norvegicus	Lysmd3	ENSRNOG00000016298
drosophila_melanogaster	CG17985	FBGN0033199
caenorhabditis_elegans	lmd-1	WBGENE00009665

Paralogs (3): LYSMD2 (ENSG00000140280), LYSMD1 (ENSG00000163155), LYSMD4 (ENSG00000183060)

Protein

Protein identifiers

LysM and putative peptidoglycan-binding domain-containing protein 3 — Q7Z3D4 (reviewed: Q7Z3D4)

All UniProt accessions (3): Q7Z3D4, A8K613, G5E9N8

UniProt curated annotations — full annotation on UniProt →

Function. Essential for Golgi structural integrity.

Subcellular location. Cell membrane. Golgi apparatus.

Induction. Up-regulated by Golgi stress-inducing agent nigericin.

Isoforms (3)

UniProt ID	Names	Canonical?
Q7Z3D4-1	1	yes
Q7Z3D4-2	2
Q7Z3D4-3	3

RefSeq proteins (2): NP_001273741, NP_938014* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018392	LysM	Domain
IPR036779	LysM_dom_sf	Homologous_superfamily
IPR045030	LYSM1-4	Family

Pfam: PF01476

UniProt features (11 total): splice variant 4, topological domain 2, chain 1, transmembrane region 1, domain 1, modified residue 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z3D4-F1	63.28	0.10

Functional residue map

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

Post-translational modifications (1): 55

Glycosylation sites (1): 7

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 153 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOMF_GLYCOSAMINOGLYCAN_BINDING, CUI_TCF21_TARGETS_2_DN, TGCCTTA_MIR124A, GOBP_GOLGI_ORGANIZATION, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, NUYTTEN_NIPP1_TARGETS_DN, GEORGES_TARGETS_OF_MIR192_AND_MIR215, YOSHIMURA_MAPK8_TARGETS_DN, GOMF_PEPTIDOGLYCAN_BINDING, WONG_ADULT_TISSUE_STEM_MODULE, DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN, JOHNSTONE_PARVB_TARGETS_3_DN

GO Biological Process (1): Golgi organization (GO:0007030)

GO Molecular Function (1): peptidoglycan binding (GO:0042834)

GO Cellular Component (4): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
organelle organization	1
endomembrane system organization	1
glycosaminoglycan binding	1
Golgi apparatus	1
bounding membrane of organelle	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

442 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LYSMD3	MBLAC2	Q68D91	608
LYSMD3	ARRDC3	Q96B67	515
LYSMD3	ADGRV1	Q8WXG9	500
LYSMD3	FAM174B	Q3ZCQ3	496
LYSMD3	A0A024R161	A0A024R161	468
LYSMD3	PCDH18	Q9HCL0	458
LYSMD3	POLR3G	O15318	448
LYSMD3	LYSMD2	Q8IV50	431
LYSMD3	ARL6IP1	Q15041	412
LYSMD3	CETN3	O15182	402
LYSMD3	SPRYD4	Q8WW59	378
LYSMD3	TMEM62	Q0P6H9	373
LYSMD3	SPRYD7	Q5W111	357
LYSMD3	TMEM121	Q9BTD3	356
LYSMD3	LYSMD1	Q96S90	351

IntAct

6 interactions, top by confidence:

A	B	Type	Score
LYSMD3	ACTA2	psi-mi:“MI:0915”(physical association)	0.400
BMP2K	LYSMD3	psi-mi:“MI:0915”(physical association)	0.370
TMEM17	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
TMEM216	GPR89A	psi-mi:“MI:2364”(proximity)	0.270
CFTR	UBA6	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (27): LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS), LYSMD3 (Proximity Label-MS)

ESM2 similar proteins: A0JNI1, E9Q0S6, O94983, O95402, P80192, Q08AE8, Q1JQA8, Q1LZH7, Q28DG6, Q3B7I8, Q3KPL3, Q3U1V8, Q4VAC9, Q53LP3, Q5BJT1, Q5DU25, Q5HZA4, Q5JU85, Q5M836, Q5PQ30, Q5RBI7, Q5REP3, Q5XG99, Q5ZKK0, Q69YU3, Q6DCC7, Q6DEF4, Q6IPM2, Q6IQA2, Q6P606, Q76G19, Q7TSI1, Q7Z3D4, Q80Y50, Q86UU1, Q8BL43, Q8BY98, Q8C0J6, Q8CC84, Q8IV50

Diamond homologs: Q28DG6, Q5M836, Q5REP3, Q5XG99, Q5ZKK0, Q6DCC7, Q6IQA2, Q6P606, Q7Z3D4, Q8CC84, Q99LE3, Q9FZ32, Q6DEF4, Q5HGI5, Q6G9W6, Q7A123, Q7A5Y8, Q99UM3, Q9ZNI1, Q5HZA4, Q96S90, Q9D0E3, Q9N012, A0JNI1, O31681, Q1JQA8, Q3B7I8, Q3KPL3, Q5PQ30, Q8IV50, Q9D7V2

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	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

620 predictions. Top by Δscore:

Variant	Effect	Δscore
5:90519300:G:C	donor_gain	1.0000
5:90519312:T:A	donor_gain	1.0000
5:90519362:T:TA	donor_gain	1.0000
5:90525028:AACTT:A	donor_loss	0.9900
5:90525029:ACTTA:A	donor_loss	0.9900
5:90525030:CTT:C	donor_loss	0.9900
5:90525031:TTACC:T	donor_loss	0.9900
5:90525032:T:TG	donor_loss	0.9900
5:90525033:A:AC	donor_gain	0.9900
5:90525033:A:C	donor_loss	0.9900
5:90525034:C:A	donor_loss	0.9900
5:90525034:C:CC	donor_gain	0.9900
5:90525034:CCGTA:C	donor_gain	0.9900
5:90529443:TTTA:T	donor_loss	0.9900
5:90529444:TTA:T	donor_loss	0.9900
5:90529446:A:C	donor_loss	0.9900
5:90529447:C:A	donor_loss	0.9900
5:90519252:T:TA	donor_gain	0.9800
5:90525027:AAACT:A	donor_loss	0.9800
5:90525134:T:TA	donor_gain	0.9700
5:90526110:T:A	donor_gain	0.9700
5:90519264:C:CT	donor_gain	0.9500
5:90519265:T:TT	donor_gain	0.9500
5:90526093:T:A	donor_gain	0.9500
5:90525301:C:CC	acceptor_gain	0.9400
5:90529016:T:TA	donor_gain	0.9300
5:90519308:AATTT:A	donor_gain	0.9100
5:90520359:A:AC	donor_gain	0.9100
5:90525299:ATCT:A	acceptor_loss	0.9100
5:90525300:TCTGG:T	acceptor_loss	0.9100

AlphaMissense

2012 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:90519456:A:G	L95P	1.000
5:90519470:C:A	K90N	1.000
5:90519470:C:G	K90N	1.000
5:90525054:G:T	A79D	1.000
5:90519042:G:C	P233R	0.999
5:90519042:G:T	P233Q	0.999
5:90519054:C:T	G229D	0.999
5:90519055:C:G	G229R	0.999
5:90519066:A:C	M225R	0.999
5:90519066:A:T	M225K	0.999
5:90519078:G:T	A221D	0.999
5:90519432:G:T	A103D	0.999
5:90519461:G:C	N93K	0.999
5:90519461:G:T	N93K	0.999
5:90519462:T:A	N93I	0.999
5:90519045:G:T	T232K	0.998
5:90519048:A:T	I231K	0.998
5:90519051:A:C	I230R	0.998
5:90519051:A:T	I230K	0.998
5:90519069:A:T	I224K	0.998
5:90519088:A:G	W218R	0.998
5:90519088:A:T	W218R	0.998
5:90519474:A:T	I89N	0.998
5:90525051:A:G	L80P	0.998
5:90525055:C:G	A79P	0.998
5:90525066:A:G	L75S	0.998
5:90519045:G:C	T232R	0.997
5:90519414:A:C	I109S	0.997
5:90519414:A:G	I109T	0.997
5:90519429:A:G	L104P	0.997

dbSNP variants (sampled 300 via entrez): RS1000879498 (5:90521381 G>C), RS1001030342 (5:90529186 G>A), RS1001460754 (5:90521158 C>G), RS1001566169 (5:90528776 A>G), RS1002247854 (5:90518078 A>C), RS1002259136 (5:90527726 A>G), RS1002320171 (5:90518460 A>G,T), RS1002525837 (5:90523480 C>T), RS1002583386 (5:90516545 CTT>C), RS1002737723 (5:90528322 T>G), RS1002876491 (5:90524378 T>A), RS1002948767 (5:90524696 A>G), RS1003029682 (5:90529864 A>G), RS1003282353 (5:90526346 T>C), RS1003666146 (5:90525923 T>A,C)

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

1 associations (top):

Study	Trait	p-value
GCST009391_402	Metabolite levels	9.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010386	phosphatidylcholine 38:4 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

35 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases expression	4
Air Pollutants	affects expression, increases abundance, decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
FR900359	increases phosphorylation	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
arsenite	affects binding, decreases reaction	1
butyraldehyde	decreases expression	1
pentanal	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	increases expression	1
bisphenol S	affects cotreatment, decreases methylation	1
jinfukang	decreases expression	1
NSC 689534	affects binding, increases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Arsenic	increases abundance, decreases methylation	1
Benzo(a)pyrene	affects methylation	1
Caffeine	decreases phosphorylation	1
Copper	affects binding, increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Dimethyl Sulfoxide	decreases expression	1
Diuron	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Hydrogen Peroxide	increases expression	1
Methyl Methanesulfonate	increases expression	1
Nicotine	affects response to substance	1
Ozone	increases abundance, affects expression	1
Tobacco Smoke Pollution	increases expression	1

Clinical trials (associated diseases)

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