LYPD2

Summary

LYPD2 (LY6/PLAUR domain containing 2, HGNC:25215) is a protein-coding gene on chromosome 8q24.3, encoding Ly6/PLAUR domain-containing protein 2 (Q6UXB3).

Predicted to be located in extracellular region and plasma membrane.

Source: NCBI Gene 137797 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_205545

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25215
Approved symbol	LYPD2
Name	LY6/PLAUR domain containing 2
Location	8q24.3
Locus type	gene with protein product
Status	Approved
Aliases	RGTR430, UNQ430
Ensembl gene	ENSG00000197353
Ensembl biotype	protein_coding
Entrez	137797

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000359228

RefSeq mRNA: 1 — MANE Select: NM_205545 NM_205545

CCDS: CCDS6388

Canonical transcript exons

ENST00000359228 — 3 exons

Exon	Start	End
ENSE00001427062	142752394	142752532
ENSE00001431227	142750150	142750482
ENSE00001433625	142751051	142751170

Expression profiles

Bgee: expression breadth broad, 92 present calls, max score 99.45.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 2.4816 / max 592.8252, expressed in 162 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
95421	1.9682	141
95422	0.5081	88
95423	0.0054	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	99.45	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	98.96	gold quality
esophagus mucosa	UBERON:0002469	95.68	gold quality
skin of leg	UBERON:0001511	83.83	gold quality
granulocyte	CL:0000094	82.97	gold quality
zone of skin	UBERON:0000014	82.79	gold quality
skin of abdomen	UBERON:0001416	81.63	gold quality
leukocyte	CL:0000738	78.78	gold quality
monocyte	CL:0000576	78.71	gold quality
vagina	UBERON:0000996	75.13	gold quality
esophagus	UBERON:0001043	72.54	gold quality
tonsil	UBERON:0002372	63.37	gold quality
right atrium auricular region	UBERON:0006631	62.61	gold quality
blood	UBERON:0000178	62.10	gold quality
right coronary artery	UBERON:0001625	60.57	gold quality
apex of heart	UBERON:0002098	60.29	gold quality
right lung	UBERON:0002167	58.55	gold quality
heart left ventricle	UBERON:0002084	58.43	gold quality
ectocervix	UBERON:0012249	58.43	gold quality
heart	UBERON:0000948	57.31	gold quality
body of stomach	UBERON:0001161	54.64	gold quality
stomach	UBERON:0000945	54.36	gold quality
uterine cervix	UBERON:0000002	53.84	gold quality
right lobe of liver	UBERON:0001114	53.31	gold quality
minor salivary gland	UBERON:0001830	52.92	gold quality
liver	UBERON:0002107	52.84	gold quality
mucosa of stomach	UBERON:0001199	51.21	gold quality
saliva-secreting gland	UBERON:0001044	50.80	gold quality
upper lobe of left lung	UBERON:0008952	48.77	gold quality
lung	UBERON:0002048	48.54	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting LYPD2, 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-4756-3P	99.62	66.30	1319
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-6895-5P	97.05	64.96	522
HSA-MIR-1296-5P	93.94	67.71	305
HSA-MIR-375-5P	72.41	65.52	3

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lypd2	ENSMUSG00000022595
rattus_norvegicus	Lypd2	ENSRNOG00000006058

Paralogs (3): CD59 (ENSG00000085063), SLURP1 (ENSG00000126233), LYPD1 (ENSG00000150551)

Protein

Protein identifiers

Ly6/PLAUR domain-containing protein 2 — Q6UXB3 (reviewed: Q6UXB3)

All UniProt accessions (2): F1T0L0, Q6UXB3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell membrane.

RefSeq proteins (1): NP_991108* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR016054	LY6_UPA_recep-like	Domain
IPR018363	CD59_antigen_CS	Conserved_site
IPR035076	Toxin/TOLIP	Domain
IPR045860	Snake_toxin-like_sf	Homologous_superfamily
IPR051110	Ly-6/neurotoxin-like_GPI-ap	Family

Pfam: PF00087

UniProt features (10 total): sequence variant 2, sequence conflict 2, signal peptide 1, chain 1, propeptide 1, domain 1, lipid moiety-binding region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UXB3-F1	75.97	0.39

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): 103

Glycosylation sites (1): 46

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-163125	Post-translational modification: synthesis of GPI-anchored proteins
R-HSA-392499	Metabolism of proteins
R-HSA-597592	Post-translational protein modification

MSigDB gene sets: 39 (showing top): DARWICHE_SKIN_TUMOR_PROMOTER_UP, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_UP, DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, GOCC_SIDE_OF_MEMBRANE, NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON, MIKKELSEN_IPS_HCP_WITH_H3_UNMETHYLATED, REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED, MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED, MARTENS_TRETINOIN_RESPONSE_UP, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, chr8q24, REACTOME_POST_TRANSLATIONAL_MODIFICATION_SYNTHESIS_OF_GPI_ANCHORED_PROTEINS

GO Biological Process (0):

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

GO Cellular Component (4): extracellular region (GO:0005576), plasma membrane (GO:0005886), side of membrane (GO:0098552), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Post-translational protein modification	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
membrane	2
binding	1
cell periphery	1
leaflet of membrane bilayer	1

Protein interactions and networks

STRING

676 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LYPD2	LY6K	Q17RY6	795
LYPD2	LYNX1	P0DP58	776
LYPD2	LY6H	O94772	711
LYPD2	PATE3	B3GLJ2	598
LYPD2	LY6L	H3BQJ8	593
LYPD2	LYPD4	Q6UWN0	586
LYPD2	DRC12	Q494R4	577
LYPD2	LYPD5	Q6UWN5	571
LYPD2	PATE2	Q6UY27	543
LYPD2	PATE4	P0C8F1	541
LYPD2	CFAP263	Q9H0I3	531
LYPD2	PINLYP	A6NC86	526
LYPD2	PSCA	O43653	511
LYPD2	PATE1	Q8WXA2	506
LYPD2	PPDPFL	Q8WWR9	485

IntAct

5 interactions, top by confidence:

A	B	Type	Score
POU4F2	LYPD2	psi-mi:“MI:0915”(physical association)	0.560
LYPD2	PLXNA2	psi-mi:“MI:0914”(association)	0.350
POU4F2	LYPD2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (8): LYPD2 (Two-hybrid), ADAM9 (Affinity Capture-MS), TMEM132A (Affinity Capture-MS), PLXNA2 (Affinity Capture-MS), GLB1L (Affinity Capture-MS), LONP2 (Affinity Capture-MS), ARSB (Affinity Capture-MS), CARS2 (Affinity Capture-MS)

ESM2 similar proteins: A0JNB3, A0JNL5, H2LID1, H3BJG9, O55186, O77541, O94772, O95867, P05533, P0CW03, P0DPQ9, P0DTL4, P13987, P27274, P35456, P35459, P35460, P46657, P47777, P49616, P51447, P57096, P58019, P83106, P83107, Q03405, Q05588, Q14210, Q148C3, Q28216, Q28785, Q32PB3, Q4R5M8, Q5R510, Q63317, Q6UWN5, Q6UXB3, Q80ZQ0, Q8SQ46, Q8TDM5

Diamond homologs: O43653, P0DP58, P57096, Q16553, Q6UXB3, Q90986, P0DP57, P0DP59, P0DP61, Q9CWP4, P55000, P58019, Q9DD23, Q9Z0K7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	31
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

642 predictions. Top by Δscore:

Variant	Effect	Δscore
8:142750481:CA:C	acceptor_gain	1.0000
8:142750483:C:CC	acceptor_gain	1.0000
8:142751045:A:AC	donor_gain	1.0000
8:142751046:C:CC	donor_gain	1.0000
8:142751047:TGA:T	donor_loss	1.0000
8:142751048:GAC:G	donor_loss	1.0000
8:142751049:A:AC	donor_gain	1.0000
8:142751049:A:AT	donor_loss	1.0000
8:142751050:C:CC	donor_gain	1.0000
8:142751050:CCTAT:C	donor_gain	1.0000
8:142751053:ATCT:A	donor_gain	1.0000
8:142751053:ATCTC:A	donor_gain	1.0000
8:142751054:T:C	donor_gain	1.0000
8:142751078:TGC:T	donor_gain	1.0000
8:142751166:CGGCG:C	acceptor_gain	1.0000
8:142751167:GGCG:G	acceptor_gain	1.0000
8:142751168:GCG:G	acceptor_gain	1.0000
8:142751169:CG:C	acceptor_gain	1.0000
8:142751169:CGC:C	acceptor_gain	1.0000
8:142751170:GCTGG:G	acceptor_loss	1.0000
8:142751171:C:A	acceptor_loss	1.0000
8:142751171:C:CC	acceptor_gain	1.0000
8:142750478:GTACA:G	acceptor_gain	0.9900
8:142750479:TACA:T	acceptor_gain	0.9900
8:142750480:ACA:A	acceptor_gain	0.9900
8:142750481:CAC:C	acceptor_gain	0.9900
8:142750490:G:C	acceptor_gain	0.9900
8:142750490:G:GC	acceptor_gain	0.9900
8:142751057:C:CA	donor_gain	0.9900
8:142751079:G:A	donor_gain	0.9900

AlphaMissense

782 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:142750472:G:C	F63L	0.944
8:142750472:G:T	F63L	0.944
8:142750474:A:G	F63L	0.944
8:142750448:C:A	K71N	0.921
8:142750448:C:G	K71N	0.921
8:142750361:A:C	N100K	0.896
8:142750361:A:T	N100K	0.896
8:142750447:A:G	S72P	0.892
8:142751080:C:G	C50S	0.888
8:142751081:A:T	C50S	0.888
8:142750365:C:G	C99S	0.882
8:142750366:A:T	C99S	0.882
8:142750473:A:C	F63C	0.881
8:142750431:C:G	C77S	0.839
8:142750432:A:T	C77S	0.839
8:142751155:C:G	C25S	0.832
8:142751156:A:T	C25S	0.832
8:142750443:C:G	C73S	0.818
8:142750444:A:T	C73S	0.818
8:142750432:A:G	C77R	0.812
8:142750380:C:G	C94S	0.808
8:142750381:A:T	C94S	0.808
8:142750441:C:G	A74P	0.802
8:142751118:A:C	C37W	0.794
8:142750365:C:T	C99Y	0.788
8:142751154:G:C	C25W	0.786
8:142751081:A:G	C50R	0.783
8:142750479:T:C	Y61C	0.782
8:142751079:G:C	C50W	0.782
8:142750366:A:G	C99R	0.780

dbSNP variants (sampled 300 via entrez): RS1000761809 (8:142750054 T>G), RS1001374248 (8:142752217 C>G,T), RS1001429869 (8:142751993 T>A,C,G), RS1001741463 (8:142752595 C>A,G,T), RS1002005133 (8:142751347 G>A,T), RS1003754941 (8:142750306 G>T), RS1004243231 (8:142753106 G>A), RS1004325864 (8:142750755 C>A,G,T), RS1005236454 (8:142751410 G>T), RS1005487952 (8:142751257 G>A), RS1006550648 (8:142750640 G>A), RS1007576072 (8:142752543 G>A), RS1007670946 (8:142752792 G>T), RS1008691414 (8:142753867 C>T), RS1009242353 (8:142753535 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

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	affects expression, decreases expression	2
sodium arsenate	decreases expression, increases abundance	1
sodium arsenite	increases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
(+)-JQ1 compound	decreases expression	1
Air Pollutants	increases abundance, decreases expression	1
Arsenic	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Diazinon	decreases methylation	1
Methapyrilene	increases methylation	1
Smoke	decreases expression, increases abundance	1
Urethane	decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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