LYSMD1

Summary

LYSMD1 (LysM domain containing 1, HGNC:32070) is a protein-coding gene on chromosome 1q21.3, encoding LysM and putative peptidoglycan-binding domain-containing protein 1 (Q96S90).

Located in nucleoplasm.

Source: NCBI Gene 388695 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 64 total
• MANE Select transcript: NM_212551

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32070
Approved symbol	LYSMD1
Name	LysM domain containing 1
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Aliases	SB145, MGC35223, RP11-68I18.5
Ensembl gene	ENSG00000163155
Ensembl biotype	protein_coding
Entrez	388695

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000368908, ENST00000440902

RefSeq mRNA: 2 — MANE Select: NM_212551 NM_001136543, NM_212551

CCDS: CCDS44218, CCDS986

Canonical transcript exons

ENST00000368908 — 3 exons

Exon	Start	End
ENSE00001072119	151161736	151162100
ENSE00001448267	151165079	151165902
ENSE00002162356	151159748	151161020

Expression profiles

Bgee: expression breadth ubiquitous, 187 present calls, max score 94.80.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.6098 / max 71.5713, expressed in 1563 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
14410	4.4842	1478
14409	0.7747	466
14411	0.3508	165

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	94.80	gold quality
tendon of biceps brachii	UBERON:0008188	87.68	gold quality
cortical plate	UBERON:0005343	85.73	gold quality
ganglionic eminence	UBERON:0004023	84.38	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.22	gold quality
hindlimb stylopod muscle	UBERON:0004252	82.12	gold quality
ventricular zone	UBERON:0003053	81.86	gold quality
oviduct epithelium	UBERON:0004804	81.76	gold quality
muscle of leg	UBERON:0001383	80.82	gold quality
prefrontal cortex	UBERON:0000451	80.61	gold quality
medial globus pallidus	UBERON:0002477	80.58	gold quality
gastrocnemius	UBERON:0001388	80.57	gold quality
left ovary	UBERON:0002119	79.82	gold quality
right ovary	UBERON:0002118	79.62	gold quality
right adrenal gland cortex	UBERON:0035827	79.44	gold quality
right adrenal gland	UBERON:0001233	79.33	gold quality
heart left ventricle	UBERON:0002084	78.95	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.72	gold quality
cardiac ventricle	UBERON:0002082	78.47	gold quality
islet of Langerhans	UBERON:0000006	78.28	gold quality
apex of heart	UBERON:0002098	78.25	gold quality
tendon	UBERON:0000043	78.21	gold quality
tibialis anterior	UBERON:0001385	78.18	silver quality
stromal cell of endometrium	CL:0002255	78.15	gold quality
left adrenal gland	UBERON:0001234	78.11	gold quality
ovary	UBERON:0000992	78.09	gold quality
ileal mucosa	UBERON:0000331	78.05	silver quality
cerebellar cortex	UBERON:0002129	77.90	gold quality
right atrium auricular region	UBERON:0006631	77.89	gold quality
mucosa of stomach	UBERON:0001199	77.87	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.55

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting LYSMD1, 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-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-5682	99.89	72.56	1005
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-548AG	99.77	69.25	1492
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-187-5P	99.74	70.26	1404
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-548AI	99.69	69.24	1494
HSA-MIR-548BA	99.69	69.14	1514
HSA-MIR-570-5P	99.69	69.24	1494
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-3153	99.55	67.59	2337
HSA-MIR-4753-5P	99.54	68.51	1356
HSA-MIR-7159-5P	99.53	72.12	2472
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-12132	99.47	68.90	1341

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lysmd1	ENSDARG00000054789
mus_musculus	Lysmd1	ENSMUSG00000053769
rattus_norvegicus		ENSRNOG00000071857
drosophila_melanogaster	CG17985	FBGN0033199
caenorhabditis_elegans	lmd-1	WBGENE00009665

Paralogs (3): LYSMD2 (ENSG00000140280), LYSMD3 (ENSG00000176018), LYSMD4 (ENSG00000183060)

Protein

Protein identifiers

LysM and putative peptidoglycan-binding domain-containing protein 1 — Q96S90 (reviewed: Q96S90)

All UniProt accessions (1): Q96S90

Isoforms (2)

UniProt ID	Names	Canonical?
Q96S90-1	1	yes
Q96S90-2	2

RefSeq proteins (2): NP_001130015, NP_997716* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF01476

UniProt features (20 total): modified residue 6, sequence conflict 3, helix 3, strand 2, region of interest 2, chain 1, domain 1, splice variant 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2DJP	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96S90-F1	66.56	0.24

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 (6): 212, 23, 33, 99, 166, 194

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 105 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, TGACCTY_ERR1_Q2, COUP_01, TCF4_Q5, HNF4_DR1_Q3, HNF4_01, PPAR_DR1_Q2, LYF1_01, RFX1_02, chr1q21, PPARG_01, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, STAT1_02

GO Biological Process (0):

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

GO Cellular Component (1): nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

234 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LYSMD1	PHLDB3	Q6NSJ2	513
LYSMD1	SCNM1	Q9BWG6	469
LYSMD1	TCEAL4	Q96EI5	419
LYSMD1	LRP5L	A4QPB2	418
LYSMD1	ANKRD49	Q8WVL7	415
LYSMD1	HMCES	Q96FZ2	396
LYSMD1	FAM168B	A1KXE4	394
LYSMD1	ZNF250	P15622	374
LYSMD1	UBE2Z	Q9H832	373
LYSMD1	ZNF426	Q9BUY5	370
LYSMD1	RNF44	Q7L0R7	370
LYSMD1	RFTN2	Q52LD8	370
LYSMD1	ZNF713	Q8N859	366
LYSMD1	GFOD1	Q9NXC2	366
LYSMD1	C17orf99	Q6UX52	357

IntAct

38 interactions, top by confidence:

A	B	Type	Score
GOLGA2	LYSMD1	psi-mi:“MI:0915”(physical association)	0.560
MTUS2	LYSMD1	psi-mi:“MI:0915”(physical association)	0.560
TCF12	LYSMD1	psi-mi:“MI:0915”(physical association)	0.560
LYSMD1	TCF12	psi-mi:“MI:0915”(physical association)	0.560
LYSMD1	GOLGA2	psi-mi:“MI:0915”(physical association)	0.560
TRIM69	LYSMD1	psi-mi:“MI:0915”(physical association)	0.560
PAX6	LYSMD1	psi-mi:“MI:0915”(physical association)	0.560
LYSMD1	TFIP11	psi-mi:“MI:0915”(physical association)	0.560
RINT1	LYSMD1	psi-mi:“MI:0915”(physical association)	0.560
TRAF2	LYSMD1	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	LYSMD1	psi-mi:“MI:0915”(physical association)	0.560
KRT34	LYSMD1	psi-mi:“MI:0915”(physical association)	0.560
DUSP4	LYSMD1	psi-mi:“MI:0915”(physical association)	0.560
LYSMD1	H1-4	psi-mi:“MI:0915”(physical association)	0.400
LYSMD1		psi-mi:“MI:0915”(physical association)	0.370
TULP3	PPP1R12A	psi-mi:“MI:0914”(association)	0.350
LYSMD1	TRIM69	psi-mi:“MI:0915”(physical association)	0.000
LYSMD1	PAX6	psi-mi:“MI:0915”(physical association)	0.000
LYSMD1	TFIP11	psi-mi:“MI:0915”(physical association)	0.000
LYSMD1	RINT1	psi-mi:“MI:0915”(physical association)	0.000
LYSMD1	TRAF2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (15): LYSMD1 (Two-hybrid), LYSMD1 (Two-hybrid), LYSMD1 (Two-hybrid), LYSMD1 (Affinity Capture-MS), LYSMD1 (Two-hybrid), LYSMD1 (Two-hybrid), LYSMD1 (Two-hybrid), LYSMD1 (Two-hybrid), LYSMD1 (Two-hybrid), LYSMD1 (Two-hybrid), TRIM69 (Two-hybrid), GOLGA6L9 (Two-hybrid), LYSMD1 (Proximity Label-MS), LYSMD1 (Affinity Capture-MS), LYSMD1 (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, Q28DG6, Q5M836, Q5REP3, Q5XG99, Q5ZKK0, Q6IQA2, Q7Z3D4, Q8CC84, Q99LE3, O31681, Q9FZ32

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	1
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

770 predictions. Top by Δscore:

Variant	Effect	Δscore
1:151161017:TACC:T	acceptor_gain	1.0000
1:151161019:CC:C	acceptor_gain	1.0000
1:151161020:CC:C	acceptor_gain	1.0000
1:151161729:GACTC:G	donor_loss	1.0000
1:151161730:ACTCA:A	donor_loss	1.0000
1:151161731:CTCAC:C	donor_loss	1.0000
1:151161732:TCACC:T	donor_loss	1.0000
1:151161733:CACCC:C	donor_loss	1.0000
1:151161734:A:AC	donor_gain	1.0000
1:151161734:AC:A	donor_gain	1.0000
1:151161735:C:CC	donor_gain	1.0000
1:151161735:C:T	donor_loss	1.0000
1:151161735:CC:C	donor_gain	1.0000
1:151162097:CCAT:C	acceptor_gain	1.0000
1:151162098:CAT:C	acceptor_gain	1.0000
1:151162098:CATC:C	acceptor_gain	1.0000
1:151162101:C:CC	acceptor_gain	1.0000
1:151162102:T:C	acceptor_gain	1.0000
1:151162102:T:TC	acceptor_gain	1.0000
1:151161016:GTACC:G	acceptor_gain	0.9900
1:151161018:ACC:A	acceptor_gain	0.9900
1:151161019:CCC:C	acceptor_gain	0.9900
1:151161021:C:CC	acceptor_gain	0.9900
1:151161021:CTGC:C	acceptor_loss	0.9900
1:151161022:T:A	acceptor_loss	0.9900
1:151161027:T:C	acceptor_gain	0.9900
1:151161027:T:TC	acceptor_gain	0.9900
1:151161728:AGACT:A	donor_loss	0.9900
1:151161734:ACC:A	donor_gain	0.9900
1:151161735:CCC:C	donor_gain	0.9900

AlphaMissense

1449 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:151162086:T:A	K65N	0.997
1:151162086:T:G	K65N	0.997
1:151162072:A:G	L70P	0.994
1:151162077:G:C	N68K	0.993
1:151162077:G:T	N68K	0.993
1:151162084:C:G	R66P	0.993
1:151162030:A:T	I84N	0.992
1:151162050:G:C	F77L	0.992
1:151162050:G:T	F77L	0.992
1:151162052:A:G	F77L	0.992
1:151162030:A:G	I84T	0.991
1:151162090:A:C	I64S	0.991
1:151162078:T:A	N68I	0.990
1:151161787:A:G	I165T	0.989
1:151162030:A:C	I84S	0.989
1:151162075:C:G	R69P	0.988
1:151162090:A:T	I64N	0.988
1:151162036:A:T	L82H	0.985
1:151165098:G:T	A54E	0.985
1:151165099:C:G	A54P	0.985
1:151161810:G:C	F157L	0.984
1:151161810:G:T	F157L	0.984
1:151161812:A:G	F157L	0.984
1:151162090:A:G	I64T	0.984
1:151165095:A:G	L55P	0.984
1:151160891:G:C	F225L	0.983
1:151160891:G:T	F225L	0.983
1:151160893:A:G	F225L	0.983
1:151161808:A:G	L158P	0.983
1:151162036:A:G	L82P	0.982

dbSNP variants (sampled 300 via entrez): RS1000400084 (1:151150484 C>G), RS1000448949 (1:151151677 C>T), RS1000543735 (1:151151343 C>G,T), RS1000605489 (1:151158487 A>T), RS1000901120 (1:151164922 T>G), RS1000935360 (1:151152637 T>C,G), RS1001309604 (1:151164080 G>C), RS1001861457 (1:151163583 T>C), RS1001958022 (1:151152172 C>T), RS1002040275 (1:151156733 G>A), RS1002178677 (1:151165932 C>T), RS1002454389 (1:151151798 G>A), RS1002534050 (1:151160404 C>CA), RS1002956926 (1:151160726 G>A,T), RS1003029571 (1:151166721 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, decreases methylation	2
Cadmium Chloride	increases expression	2
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
ferrous chloride	increases expression	1
CGP 52608	affects binding, increases reaction	1
Cannabidiol	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Urethane	affects expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Asbestos, Crocidolite	decreases expression	1

Clinical trials (associated diseases)

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