LYSMD4

Summary

LYSMD4 (LysM domain containing 4, HGNC:26571) is a protein-coding gene on chromosome 15q26.3, encoding LysM and putative peptidoglycan-binding domain-containing protein 4 (Q5XG99).

Predicted to be located in membrane.

Source: NCBI Gene 145748 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 59 total — 2 pathogenic
• MANE Select transcript: NM_001284417

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26571
Approved symbol	LYSMD4
Name	LysM domain containing 4
Location	15q26.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ33008
Ensembl gene	ENSG00000183060
Ensembl biotype	protein_coding
Entrez	145748

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 13 protein_coding, 3 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000332728, ENST00000344791, ENST00000378904, ENST00000409796, ENST00000450512, ENST00000479791, ENST00000484050, ENST00000493256, ENST00000496108, ENST00000545021, ENST00000604213, ENST00000684762, ENST00000878882, ENST00000878883, ENST00000878884, ENST00000878885, ENST00000878886, ENST00000924134

RefSeq mRNA: 7 — MANE Select: NM_001284417 NM_001284417, NM_001284418, NM_001284419, NM_001284420, NM_001284421, NM_001284422, NM_152449

CCDS: CCDS10381, CCDS66876, CCDS66877, CCDS73788

Canonical transcript exons

ENST00000684762 — 3 exons

Exon	Start	End
ENSE00001585261	99727405	99729731
ENSE00001781053	99733345	99733437
ENSE00003689589	99731718	99732007

Expression profiles

Bgee: expression breadth ubiquitous, 198 present calls, max score 88.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.9533 / max 54.2742, expressed in 1547 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
151769	3.9533	1547

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	88.55	gold quality
ileal mucosa	UBERON:0000331	87.97	silver quality
right hemisphere of cerebellum	UBERON:0014890	86.65	gold quality
cerebellar hemisphere	UBERON:0002245	85.91	gold quality
skin of leg	UBERON:0001511	85.88	gold quality
Brodmann (1909) area 9	UBERON:0013540	85.72	gold quality
cerebellar cortex	UBERON:0002129	85.69	gold quality
right frontal lobe	UBERON:0002810	85.65	gold quality
skin of abdomen	UBERON:0001416	85.20	gold quality
primary visual cortex	UBERON:0002436	84.84	gold quality
right atrium auricular region	UBERON:0006631	84.37	gold quality
zone of skin	UBERON:0000014	84.29	gold quality
cerebellum	UBERON:0002037	84.07	gold quality
lower esophagus mucosa	UBERON:0035834	83.98	gold quality
skin of hip	UBERON:0001554	83.75	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.27	gold quality
anterior cingulate cortex	UBERON:0009835	83.23	gold quality
upper arm skin	UBERON:0004263	83.17	gold quality
gastrocnemius	UBERON:0001388	83.05	gold quality
esophagus mucosa	UBERON:0002469	82.93	gold quality
cardiac atrium	UBERON:0002081	82.84	gold quality
body of uterus	UBERON:0009853	82.67	gold quality
muscle of leg	UBERON:0001383	82.58	gold quality
lower esophagus	UBERON:0013473	82.42	gold quality
lower esophagus muscularis layer	UBERON:0035833	82.41	gold quality
esophagus	UBERON:0001043	82.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	82.28	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	82.28	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	82.24	gold quality
heart left ventricle	UBERON:0002084	81.99	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

49 targeting LYSMD4, 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-590-3P	99.96	74.34	6478
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-18A-3P	99.56	65.68	1092
HSA-MIR-4735-5P	99.43	68.49	1780
HSA-MIR-377-3P	99.37	70.18	1905
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-542-3P	99.34	67.58	1270
HSA-MIR-520F-5P	99.34	70.40	1632
HSA-MIR-6505-3P	99.34	67.39	1071
HSA-MIR-3678-3P	99.31	67.10	1432
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-6837-5P	99.25	65.47	1632
HSA-MIR-4685-5P	99.25	65.99	1563
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-5190	99.15	67.76	1234
HSA-MIR-3125	99.14	68.49	2269
HSA-MIR-6749-3P	99.00	65.73	1443
HSA-MIR-320A-5P	98.88	66.75	1248
HSA-MIR-29B-1-5P	98.86	68.35	1364
HSA-MIR-4755-3P	98.77	65.59	1915
HSA-MIR-6794-3P	98.76	66.99	894
HSA-MIR-4763-5P	98.75	63.89	854
HSA-MIR-4463	98.56	66.05	1071

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lysmd4	ENSDARG00000068702
mus_musculus	Lysmd4	ENSMUSG00000043831
rattus_norvegicus	Lysmd4	ENSRNOG00000050624
drosophila_melanogaster	CG17985	FBGN0033199
caenorhabditis_elegans	lmd-1	WBGENE00009665

Paralogs (3): LYSMD2 (ENSG00000140280), LYSMD1 (ENSG00000163155), LYSMD3 (ENSG00000176018)

Protein

Protein identifiers

LysM and putative peptidoglycan-binding domain-containing protein 4 — Q5XG99 (reviewed: Q5XG99)

All UniProt accessions (5): Q5XG99, B3KWE4, C9J1B9, F6SJM1, Q6MZR2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5XG99-1	1	yes
Q5XG99-2	2

RefSeq proteins (7): NP_001271346, NP_001271347, NP_001271348, NP_001271349, NP_001271350, NP_001271351, NP_689662 (=MANE)

Domains & families (InterPro)

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

UniProt features (13 total): sequence variant 3, topological domain 2, chain 1, sequence conflict 1, transmembrane region 1, domain 1, region of interest 1, compositionally biased region 1, glycosylation site 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5XG99-F1	63.23	0.11

Functional residue map

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

Glycosylation sites (1): 30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 30 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, BRUECKNER_TARGETS_OF_MIRLET7A3_DN, NIKOLSKY_BREAST_CANCER_15Q26_AMPLICON, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, chr15q26, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3, ATF6_TARGET_GENES, SFMBT1_TARGET_GENES, ZIM3_TARGET_GENES, MIR576_5P, MIR448, MIR520F_5P, GSE11057_CD4_EFF_MEM_VS_PBMC_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

314 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LYSMD4	LYSMD2	Q8IV50	627
LYSMD4	FAM174B	Q3ZCQ3	574
LYSMD4	STUM	Q69YW2	507
LYSMD4	PLS1	Q14651	481
LYSMD4	TMPPE	Q6ZT21	474
LYSMD4	CCDC9B	Q6ZUT6	471
LYSMD4	ST8SIA2	Q92186	428
LYSMD4	NTMT2	Q5VVY1	411
LYSMD4	HAUS4	Q9H6D7	409
LYSMD4	INKA1	Q96EL1	397
LYSMD4	ADAMTS17	Q8TE56	366
LYSMD4	TBC1D31	Q96DN5	365
LYSMD4	GPR62	Q9BZJ7	348
LYSMD4	FITM1	A5D6W6	345
LYSMD4	LYSMD1	Q96S90	339

IntAct

0 interactions, top by confidence:

BioGRID (26): LYSMD4 (Proximity Label-MS), LYSMD4 (Proximity Label-MS), LYSMD4 (Proximity Label-MS), LYSMD4 (Proximity Label-MS), LYSMD4 (Proximity Label-MS), LYSMD4 (Negative Genetic), LYSMD4 (Affinity Capture-RNA), LYSMD4 (Proximity Label-MS), LYSMD4 (Proximity Label-MS), LYSMD4 (Proximity Label-MS), LYSMD4 (Proximity Label-MS), SLC12A4 (Co-fractionation), LYSMD4 (Co-fractionation), LYSMD4 (Co-fractionation), LYSMD4 (Co-fractionation)

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, Q3B7I8, Q3KPL3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	49
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
1526475	GRCh37/hg19 15q26.3(chr15:99258367-102429112)	Pathogenic
3063384	GRCh37/hg19 15q26.1-26.3(chr15:94176550-102429112)x3	Pathogenic

SpliceAI

1020 predictions. Top by Δscore:

Variant	Effect	Δscore
15:99731712:TCTTA:T	donor_loss	1.0000
15:99731713:CTTAC:C	donor_loss	1.0000
15:99731714:TTAC:T	donor_loss	1.0000
15:99731715:TACTT:T	donor_loss	1.0000
15:99731716:A:AC	donor_gain	1.0000
15:99731717:C:CG	donor_gain	1.0000
15:99731717:CT:C	donor_gain	1.0000
15:99731717:CTTTG:C	donor_gain	1.0000
15:99732008:C:CC	acceptor_gain	1.0000
15:99729728:CAAC:C	acceptor_gain	0.9900
15:99729732:C:CA	acceptor_loss	0.9900
15:99729733:T:C	acceptor_loss	0.9900
15:99731171:A:AC	donor_gain	0.9900
15:99731172:C:CC	donor_gain	0.9900
15:99731711:GTCTT:G	donor_loss	0.9900
15:99731729:A:AC	donor_gain	0.9900
15:99731730:C:CC	donor_gain	0.9900
15:99732003:CTTCA:C	acceptor_gain	0.9900
15:99732006:CA:C	acceptor_gain	0.9900
15:99729730:AC:A	acceptor_gain	0.9800
15:99729731:CC:C	acceptor_gain	0.9800
15:99730299:T:C	acceptor_gain	0.9800
15:99731163:T:A	donor_gain	0.9800
15:99731854:C:CT	acceptor_gain	0.9800
15:99733305:C:CA	donor_gain	0.9800
15:99729732:C:CC	acceptor_gain	0.9700
15:99731199:C:CC	acceptor_gain	0.9700
15:99732006:CACTG:C	acceptor_loss	0.9700
15:99732007:AC:A	acceptor_loss	0.9700
15:99732008:C:CA	acceptor_loss	0.9700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000288442 (15:99727007 C>T), RS1000423938 (15:99726831 G>A), RS1000577811 (15:99733136 G>A,C,T), RS1000644271 (15:99732089 A>G), RS1000755241 (15:99727860 T>C,G), RS1000862821 (15:99717217 T>C), RS1000888950 (15:99725272 T>C), RS1000928948 (15:99723278 G>A,T), RS1000987931 (15:99730783 A>C), RS1001033225 (15:99732932 C>T), RS1001080930 (15:99717432 A>G), RS1001361567 (15:99722946 G>A), RS1001454443 (15:99715363 C>G,T), RS1001505247 (15:99715725 T>TAAAGA,TAAAG), RS1001999918 (15:99721425 G>A)

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
GCST001850_46	Major depressive disorder	3.000000e-06
GCST002097_25	Coronary artery calcification	4.000000e-06
GCST003265_206	Post bronchodilator FEV1/FVC ratio in COPD	4.000000e-06
GCST003265_213	Post bronchodilator FEV1/FVC ratio in COPD	2.000000e-06
GCST003265_219	Post bronchodilator FEV1/FVC ratio in COPD	2.000000e-06
GCST003265_221	Post bronchodilator FEV1/FVC ratio in COPD	1.000000e-06
GCST008521_7	Bitter beverage consumption	2.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004723	coronary artery calcification
EFO:0004713	FEV/FVC ratio
EFO:0010089	bitter beverage consumption measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	2
Valproic Acid	increases expression, increases methylation	2
GSK-J4	decreases expression	1
bisphenol A	increases methylation	1
trichostatin A	affects expression	1
sodium arsenite	affects expression	1
jinfukang	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Leflunomide	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Smoke	increases expression	1
Tamoxifen	affects cotreatment, decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	affects expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression	1
Raloxifene Hydrochloride	affects cotreatment, decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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