LYSMD2

Summary

LYSMD2 (LysM domain containing 2, HGNC:28571) is a protein-coding gene on chromosome 15q21.2, encoding LysM and putative peptidoglycan-binding domain-containing protein 2 (Q8IV50).

At a glance

• Clinical variants (ClinVar): 17 total
• MANE Select transcript: NM_153374

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28571
Approved symbol	LYSMD2
Name	LysM domain containing 2
Location	15q21.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC35274
Ensembl gene	ENSG00000140280
Ensembl biotype	protein_coding
Entrez	256586

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000267838, ENST00000454181, ENST00000558126, ENST00000560491, ENST00000875742, ENST00000875743

RefSeq mRNA: 3 — MANE Select: NM_153374 NM_001143917, NM_001363969, NM_153374

CCDS: CCDS10143, CCDS45259

Canonical transcript exons

ENST00000267838 — 3 exons

Exon	Start	End
ENSE00001262741	51737350	51737655
ENSE00001811983	51723011	51723649
ENSE00003758231	51724790	51725121

Expression profiles

Bgee: expression breadth ubiquitous, 248 present calls, max score 98.31.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.3825 / max 136.9718, expressed in 1698 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
149948	10.4686	1662
149950	2.6311	782
149949	0.1048	52
149953	0.0809	31
149954	0.0692	43
149952	0.0166	7
149951	0.0113	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pons	UBERON:0000988	98.31	gold quality
cerebellar vermis	UBERON:0004720	98.14	gold quality
lateral nuclear group of thalamus	UBERON:0002736	97.11	gold quality
superior vestibular nucleus	UBERON:0007227	96.40	gold quality
substantia nigra pars compacta	UBERON:0001965	96.23	gold quality
postcentral gyrus	UBERON:0002581	95.92	gold quality
parietal lobe	UBERON:0001872	95.74	gold quality
medulla oblongata	UBERON:0001896	95.57	gold quality
dorsal root ganglion	UBERON:0000044	95.35	gold quality
superior frontal gyrus	UBERON:0002661	95.32	gold quality
Brodmann (1909) area 46	UBERON:0006483	95.25	gold quality
substantia nigra pars reticulata	UBERON:0001966	94.85	gold quality
adult organism	UBERON:0007023	94.74	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	94.38	gold quality
Brodmann (1909) area 9	UBERON:0013540	94.23	gold quality
bronchial epithelial cell	CL:0002328	94.16	gold quality
Brodmann (1909) area 23	UBERON:0013554	94.16	gold quality
thymus	UBERON:0002370	94.02	gold quality
bronchus	UBERON:0002185	94.01	gold quality
ileal mucosa	UBERON:0000331	93.93	gold quality
leukocyte	CL:0000738	93.87	gold quality
dorsal plus ventral thalamus	UBERON:0001897	93.83	gold quality
monocyte	CL:0000576	93.77	gold quality
trigeminal ganglion	UBERON:0001675	93.76	gold quality
prefrontal cortex	UBERON:0000451	93.69	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	93.65	gold quality
frontal cortex	UBERON:0001870	93.64	gold quality
frontal lobe	UBERON:0016525	93.64	gold quality
middle temporal gyrus	UBERON:0002771	93.56	gold quality
ventral tegmental area	UBERON:0002691	93.45	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.01

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting LYSMD2, 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-5011-5P	100.00	83.46	5820
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-4320	99.75	65.80	793
HSA-MIR-3617-5P	99.75	69.41	1968
HSA-MIR-641	99.75	69.35	1975
HSA-MIR-148A-3P	99.74	73.77	1700
HSA-MIR-148B-3P	99.74	73.75	1700
HSA-MIR-152-3P	99.74	73.75	1703
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-7161-5P	99.68	68.92	1592
HSA-MIR-548U	99.65	67.78	1463
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-5009-3P	99.45	69.43	1341
HSA-MIR-4426	99.17	66.74	1949
HSA-MIR-3117-5P	99.04	67.93	618
HSA-MIR-487A-5P	98.85	69.37	993
HSA-MIR-487B-5P	98.85	69.48	987
HSA-MIR-5590-5P	98.81	68.78	969

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lysmd2	ENSDARG00000091771
mus_musculus	Lysmd2	ENSMUSG00000032184
rattus_norvegicus	Lysmd2	ENSRNOG00000010642
drosophila_melanogaster	CG17985	FBGN0033199
caenorhabditis_elegans	lmd-1	WBGENE00009665

Paralogs (3): LYSMD1 (ENSG00000163155), LYSMD3 (ENSG00000176018), LYSMD4 (ENSG00000183060)

Protein

Protein identifiers

LysM and putative peptidoglycan-binding domain-containing protein 2 — Q8IV50 (reviewed: Q8IV50)

All UniProt accessions (2): Q8IV50, H0YK98

Isoforms (2)

UniProt ID	Names	Canonical?
Q8IV50-1	1	yes
Q8IV50-2	2

RefSeq proteins (3): NP_001137389, NP_001350898, NP_699205* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF01476

UniProt features (16 total): modified residue 5, region of interest 3, sequence variant 2, compositionally biased region 2, initiator methionine 1, chain 1, splice variant 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IV50-F1	67.39	0.17

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 (5): 24, 33, 57, 2, 5

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 180 (showing top): BENPORATH_ES_WITH_H3K27ME3, TTTGTAG_MIR520D, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, LHX3_01, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, WEI_MYCN_TARGETS_WITH_E_BOX, AP1_Q4_01, MYOD_01, WANG_LMO4_TARGETS_DN, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2, IRF1_Q6, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, ZHAN_MULTIPLE_MYELOMA_LB_DN, TGANTCA_AP1_C, NRF2_Q4

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

212 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LYSMD2	LYSMD4	Q5XG99	627
LYSMD2	TIPE3	Q5GJ75	445
LYSMD2	LYSMD3	Q7Z3D4	431
LYSMD2	ATOSA	Q32MH5	376
LYSMD2	GASK1B	Q6UWH4	374
LYSMD2	ZCCHC2	Q9C0B9	360
LYSMD2	STIMATE	Q86TL2	342
LYSMD2	HAPLN3	Q96S86	339
LYSMD2	GIMAP6	Q6P9H5	303
LYSMD2	GIMAP8	Q8ND71	303
LYSMD2	ERLEC1	Q96DZ1	295
LYSMD2	SCIMP	Q6UWF3	294
LYSMD2	RNF19B	Q6ZMZ0	292
LYSMD2	TMT1B	Q6UX53	282
LYSMD2	DMXL2	Q8TDJ6	277

IntAct

13 interactions, top by confidence:

A	B	Type	Score
Mtcl2	PIPSL	psi-mi:“MI:0914”(association)	0.350
Klc3	ZC3HAV1	psi-mi:“MI:0914”(association)	0.350
Kif5b	UNC84A	psi-mi:“MI:0914”(association)	0.350
Ppp2r3a	PHLPP1	psi-mi:“MI:0914”(association)	0.350
SLAIN2	TARS3	psi-mi:“MI:0914”(association)	0.350
TWNK	RAD9A	psi-mi:“MI:0914”(association)	0.350
MZT1	ZC3H18	psi-mi:“MI:0914”(association)	0.350
HIF1A	PIAS1	psi-mi:“MI:0914”(association)	0.350
BTBD8	HSPA8	psi-mi:“MI:0914”(association)	0.350
JAK3	WDR46	psi-mi:“MI:0914”(association)	0.350
PRKCD	DHX16	psi-mi:“MI:0914”(association)	0.350
KBTBD7	DKFZp686H10254	psi-mi:“MI:0914”(association)	0.350

BioGRID (18): LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-MS), LYSMD2 (Affinity Capture-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: A0JNI1, Q1JQA8, Q3B7I8, Q3KPL3, Q5HZA4, Q5PQ30, Q6DCC7, Q6DEF4, Q8IV50, Q96S90, Q9D0E3, Q9D7V2, Q9N012, Q6P606, O31681, Q7Z3D4, Q9FZ32

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	16
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

479 predictions. Top by Δscore:

Variant	Effect	Δscore
15:51725118:CCAT:C	acceptor_gain	1.0000
15:51725119:CAT:C	acceptor_gain	1.0000
15:51725119:CATC:C	acceptor_gain	1.0000
15:51725120:ATCTA:A	acceptor_loss	1.0000
15:51725122:C:CC	acceptor_gain	1.0000
15:51725122:CTAAA:C	acceptor_loss	1.0000
15:51725123:T:A	acceptor_loss	1.0000
15:51737344:GCTCA:G	donor_loss	1.0000
15:51737345:CTCAC:C	donor_loss	1.0000
15:51737346:TCAC:T	donor_loss	1.0000
15:51737349:C:G	donor_loss	1.0000
15:51737361:A:AC	donor_gain	1.0000
15:51737362:C:CC	donor_gain	1.0000
15:51724785:CTTA:C	donor_loss	0.9900
15:51724786:TTA:T	donor_loss	0.9900
15:51724787:TAC:T	donor_loss	0.9900
15:51724788:ACCT:A	donor_loss	0.9900
15:51725117:TCCAT:T	acceptor_gain	0.9900
15:51725118:CCATC:C	acceptor_gain	0.9900
15:51725120:AT:A	acceptor_gain	0.9900
15:51725120:ATCT:A	acceptor_gain	0.9900
15:51725129:A:C	acceptor_gain	0.9900
15:51737348:A:AC	donor_gain	0.9900
15:51737349:C:CC	donor_gain	0.9900
15:51723648:CT:C	acceptor_gain	0.9800
15:51723650:C:CC	acceptor_gain	0.9800
15:51724789:CCTG:C	donor_gain	0.9800
15:51725119:CATCT:C	acceptor_gain	0.9800
15:51725127:A:AC	acceptor_gain	0.9800
15:51725129:A:AC	acceptor_gain	0.9800

AlphaMissense

1376 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:51725057:A:G	L113S	0.999
15:51725111:A:C	I95S	0.999
15:51737369:G:T	A85E	0.999
15:51737465:C:T	G53D	0.999
15:51724835:A:G	I187T	0.998
15:51725051:A:T	I115N	0.998
15:51725098:A:C	N99K	0.998
15:51725098:A:T	N99K	0.998
15:51725099:T:A	N99I	0.998
15:51725107:T:A	K96N	0.998
15:51725107:T:G	K96N	0.998
15:51725111:A:T	I95N	0.998
15:51737366:A:G	L86P	0.998
15:51737399:A:T	V75D	0.998
15:51725051:A:C	I115S	0.997
15:51725071:A:C	F108L	0.997
15:51725071:A:T	F108L	0.997
15:51725073:A:G	F108L	0.997
15:51725075:A:T	I107K	0.997
15:51725093:A:G	L101P	0.997
15:51737370:C:G	A85P	0.997
15:51737372:A:T	I84N	0.997
15:51737469:A:G	Y52H	0.997
15:51724835:A:C	I187S	0.996
15:51724856:A:G	L180P	0.996
15:51725051:A:G	I115T	0.996
15:51725111:A:G	I95T	0.996
15:51737372:A:C	I84S	0.996
15:51725089:A:C	F102L	0.995
15:51725089:A:T	F102L	0.995

dbSNP variants (sampled 300 via entrez): RS1000060921 (15:51749206 T>C), RS1000101765 (15:51752420 T>A), RS1000233169 (15:51734327 G>T), RS1000293593 (15:51728334 A>G), RS1000345366 (15:51728541 T>C), RS1000374842 (15:51725854 G>C), RS1000523762 (15:51732752 A>G), RS1000583942 (15:51734100 T>C), RS1000623391 (15:51733455 G>C,T), RS1000647451 (15:51731825 G>A), RS1000678289 (15:51727139 A>G), RS1000927203 (15:51745774 A>G), RS1001137446 (15:51727027 T>C,G), RS1001138200 (15:51739399 T>C), RS1001379771 (15:51746354 G>A,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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	5
Cyclosporine	decreases methylation, increases expression	3
Vorinostat	increases expression, affects cotreatment	2
Panobinostat	affects cotreatment, increases expression	2
Benzo(a)pyrene	affects methylation, decreases methylation, increases expression, increases methylation	2
Nickel	increases expression	2
Aflatoxin B1	decreases methylation, increases expression	2
Particulate Matter	decreases reaction, increases expression, decreases expression, increases abundance	2
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
glycidyl methacrylate	increases expression	1
sulforaphane	increases expression	1
sodium arsenite	decreases expression	1
coumarin	decreases phosphorylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
clothianidin	decreases expression	1
nutlin 3	affects cotreatment, increases expression	1
abrine	decreases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases reaction, increases expression	1
dorsomorphin	increases expression, affects cotreatment	1
jinfukang	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects methylation	1
Vehicle Emissions	decreases reaction, increases expression	1
Cisplatin	increases expression, affects cotreatment	1

Clinical trials (associated diseases)

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