LYPD5

Summary

LYPD5 (LY6/PLAUR domain containing 5, HGNC:26397) is a protein-coding gene on chromosome 19q13.31, encoding Ly6/PLAUR domain-containing protein 5 (Q6UWN5).

Predicted to be located in extracellular region. Predicted to be active in plasma membrane.

Source: NCBI Gene 284348 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 36 total
• MANE Select transcript: NM_001031749

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26397
Approved symbol	LYPD5
Name	LY6/PLAUR domain containing 5
Location	19q13.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ30469, Haldisin
Ensembl gene	ENSG00000159871
Ensembl biotype	protein_coding
OMIM	619618
Entrez	284348

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000377950, ENST00000414615, ENST00000594013, ENST00000594049, ENST00000595666, ENST00000599397, ENST00000601224, ENST00000602179, ENST00000651184

RefSeq mRNA: 3 — MANE Select: NM_001031749 NM_001031749, NM_001288763, NM_182573

CCDS: CCDS12631, CCDS46096

Canonical transcript exons

ENST00000377950 — 5 exons

Exon	Start	End
ENSE00001322724	43798812	43798988
ENSE00001475607	43795927	43797829
ENSE00002224542	43802317	43802447
ENSE00003609447	43799706	43799834
ENSE00003646530	43798455	43798601

Expression profiles

Bgee: expression breadth ubiquitous, 165 present calls, max score 91.79.

FANTOM5 (CAGE): breadth broad, TPM avg 2.3140 / max 92.7703, expressed in 442 samples.

FANTOM5 promoters (16 alternative TSS)

Promoter ID	TPM avg	Samples expressed
181371	0.6920	185
181360	0.2901	79
181370	0.2684	40
181366	0.2535	101
181367	0.1572	67
181361	0.1475	76
181368	0.1320	60
181372	0.1101	52
181362	0.1027	63
181376	0.0548	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of leg	UBERON:0001511	91.79	gold quality
skin of abdomen	UBERON:0001416	91.32	gold quality
zone of skin	UBERON:0000014	89.03	gold quality
upper arm skin	UBERON:0004263	85.74	silver quality
right frontal lobe	UBERON:0002810	81.96	gold quality
Brodmann (1909) area 9	UBERON:0013540	80.79	gold quality
anterior cingulate cortex	UBERON:0009835	80.51	gold quality
prefrontal cortex	UBERON:0000451	80.46	gold quality
buccal mucosa cell	CL:0002336	80.12	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.77	gold quality
esophagus mucosa	UBERON:0002469	78.52	gold quality
nucleus accumbens	UBERON:0001882	76.68	gold quality
hypothalamus	UBERON:0001898	76.46	gold quality
neocortex	UBERON:0001950	76.37	gold quality
frontal cortex	UBERON:0001870	76.34	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	76.25	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	75.29	gold quality
putamen	UBERON:0001874	74.37	gold quality
esophagus	UBERON:0001043	74.19	gold quality
caudate nucleus	UBERON:0001873	74.13	gold quality
cortical plate	UBERON:0005343	73.98	gold quality
amygdala	UBERON:0001876	72.95	gold quality
cerebral cortex	UBERON:0000956	72.86	gold quality
lower esophagus mucosa	UBERON:0035834	72.38	gold quality
spinal cord	UBERON:0002240	72.17	gold quality
right lung	UBERON:0002167	71.94	gold quality
upper lobe of left lung	UBERON:0008952	71.67	gold quality
right hemisphere of cerebellum	UBERON:0014890	71.46	gold quality
forebrain	UBERON:0001890	71.23	gold quality
gingiva	UBERON:0001828	71.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.72

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

56 targeting LYPD5, 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-4789-5P	99.98	70.76	2721
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-651-5P	99.64	68.49	1104
HSA-MIR-891B	99.59	69.81	1083
HSA-MIR-425-5P	99.59	67.67	900
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-4687-3P	99.48	66.41	968
HSA-MIR-5580-5P	99.38	66.96	1139
HSA-MIR-520A-5P	99.35	66.72	1632
HSA-MIR-525-5P	99.35	66.85	1615
HSA-MIR-6731-5P	99.28	67.42	2375
HSA-MIR-8085	99.28	67.56	2362
HSA-MIR-7974	99.24	65.48	1137
HSA-MIR-4478	99.07	65.16	2320
HSA-MIR-3117-5P	99.04	67.93	618
HSA-MIR-6506-5P	99.04	65.66	1386
HSA-MIR-4801	98.96	69.42	2096
HSA-MIR-4464	98.95	67.73	820
HSA-MIR-3135B	98.61	65.33	1470
HSA-MIR-12125	98.59	67.54	1044
HSA-MIR-619-5P	98.57	64.97	1988

Literature-anchored findings (GeneRIF, showing 2)

• The study identifies LYPD5 a novel differentiation marker of stratum granulosum in squamous epithelia. (PMID:23896969)
• Expression of the Ly6/uPAR-domain proteins C4.4A and Haldisin in non-invasive and invasive skin lesions (PMID:25414274)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lypd5	ENSMUSG00000030484
rattus_norvegicus	Lypd5	ENSRNOG00000019432

Paralogs (2): PLAUR (ENSG00000011422), LYPD3 (ENSG00000124466)

Protein

Protein identifiers

Ly6/PLAUR domain-containing protein 5 — Q6UWN5 (reviewed: Q6UWN5)

All UniProt accessions (3): Q6UWN5, M0QYY3, M0R1J4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6UWN5-1	1	yes
Q6UWN5-2	2

RefSeq proteins (3): NP_001026919, NP_001275692, NP_872379 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR016054	LY6_UPA_recep-like	Domain
IPR018363	CD59_antigen_CS	Conserved_site
IPR045860	Snake_toxin-like_sf	Homologous_superfamily

Pfam: PF00021

UniProt features (12 total): sequence variant 3, glycosylation site 2, signal peptide 1, chain 1, sequence conflict 1, propeptide 1, domain 1, lipid moiety-binding region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UWN5-F1	84.70	0.67

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): 225

Glycosylation sites (2): 120, 174

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: 46 (showing top): NUYTTEN_EZH2_TARGETS_DN, GOCC_SIDE_OF_MEMBRANE, REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF, REACTOME_POST_TRANSLATIONAL_MODIFICATION_SYNTHESIS_OF_GPI_ANCHORED_PROTEINS, H1_6_TARGET_GENES, HOXC6_TARGET_GENES, KLF7_TARGET_GENES, RYBP_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF184_TARGET_GENES, ZNF30_TARGET_GENES, ZNF577_TARGET_GENES, ZNF664_TARGET_GENES

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

330 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LYPD5	PINLYP	A6NC86	691
LYPD5	LY6L	H3BQJ8	670
LYPD5	PATE3	B3GLJ2	666
LYPD5	PATE2	Q6UY27	605
LYPD5	SPACA4	Q8TDM5	595
LYPD5	PATE1	Q8WXA2	583
LYPD5	PATE4	P0C8F1	583
LYPD5	TEX101	Q9BY14	582
LYPD5	LY6G5B	Q8NDX9	574
LYPD5	LYPD2	Q6UXB3	571
LYPD5	SLURP1	P55000	570
LYPD5	LY6H	O94772	570
LYPD5	ZNF511	Q8NB15	541
LYPD5	LYPD4	Q6UWN0	541
LYPD5	LY6G5C	Q5SRR4	530

IntAct

28 interactions, top by confidence:

A	B	Type	Score
ERG28	LYPD5	psi-mi:“MI:0915”(physical association)	0.560
NINJ2	LYPD5	psi-mi:“MI:0915”(physical association)	0.560
EHHADH	LYPD5	psi-mi:“MI:0915”(physical association)	0.560
LYPD5	ERG28	psi-mi:“MI:0915”(physical association)	0.560
LYPD5	ERMP1	psi-mi:“MI:0915”(physical association)	0.560
LYPD5	PLPPR2	psi-mi:“MI:0915”(physical association)	0.560
BET1	LYPD5	psi-mi:“MI:0915”(physical association)	0.560
LYPD5	NINJ2	psi-mi:“MI:0915”(physical association)	0.560
TSPO	LYPD5	psi-mi:“MI:0915”(physical association)	0.560
IFITM3	LYPD5	psi-mi:“MI:0915”(physical association)	0.560
rep	LYPD5	psi-mi:“MI:0915”(physical association)	0.490
LYPD5	CDC45	psi-mi:“MI:0914”(association)	0.350
ERMP1	LYPD5	psi-mi:“MI:0915”(physical association)	0.000
PLPPR2	LYPD5	psi-mi:“MI:0915”(physical association)	0.000
BET1	LYPD5	psi-mi:“MI:0915”(physical association)	0.000
TSPO	LYPD5	psi-mi:“MI:0915”(physical association)	0.000
IFITM3	LYPD5	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (14): CLSTN1 (Affinity Capture-MS), LYPD5 (Two-hybrid), LYPD5 (Two-hybrid), LYPD5 (Two-hybrid), LYPD5 (Two-hybrid), LYPD5 (Two-hybrid), LYPD5 (Two-hybrid), LYPD5 (Two-hybrid), NINJ2 (Two-hybrid), CDC45 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), METTL9 (Affinity Capture-MS), LYPD5 (Two-hybrid), LYPD5 (Positive Genetic)

ESM2 similar proteins: A0JNB3, A0JNL5, A6NC86, H3BJG9, H3BQJ8, O55186, O94772, O95867, P05533, P0CW02, P0CW03, P0DTL4, P13987, P35456, P35459, P35460, P35461, P46657, P47777, P49616, P57096, P58019, Q03405, Q05588, Q14210, Q148C3, Q28216, Q28785, Q32PB3, Q4R5M8, Q5R510, Q63317, Q64253, Q6UWN5, Q6UX82, Q80ZQ0, Q8K1T6, Q8SQ46, Q8TDM5, Q924B5

Diamond homologs: Q6UWN5, Q9D7Z7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	25
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

597 predictions. Top by Δscore:

Variant	Effect	Δscore
19:43798449:CCTTA:C	donor_loss	1.0000
19:43798450:CTTAC:C	donor_loss	1.0000
19:43798451:TTACC:T	donor_loss	1.0000
19:43798452:TA:T	donor_loss	1.0000
19:43798453:A:AC	donor_gain	1.0000
19:43798453:A:C	donor_loss	1.0000
19:43798454:C:CC	donor_gain	1.0000
19:43798454:CCAA:C	donor_gain	1.0000
19:43798457:A:AC	donor_gain	1.0000
19:43798458:C:CC	donor_gain	1.0000
19:43798597:GGGTG:G	acceptor_gain	1.0000
19:43798599:GTG:G	acceptor_gain	1.0000
19:43798600:TG:T	acceptor_gain	1.0000
19:43798600:TGCT:T	acceptor_loss	1.0000
19:43798601:GCTG:G	acceptor_loss	1.0000
19:43798602:C:CA	acceptor_loss	1.0000
19:43798602:C:CC	acceptor_gain	1.0000
19:43798606:C:CT	acceptor_gain	1.0000
19:43799700:CCTTA:C	donor_loss	1.0000
19:43799701:CTTAC:C	donor_loss	1.0000
19:43799702:TTACC:T	donor_loss	1.0000
19:43799703:TAC:T	donor_loss	1.0000
19:43799704:A:AC	donor_gain	1.0000
19:43799704:ACCGG:A	donor_loss	1.0000
19:43799705:C:CC	donor_gain	1.0000
19:43810116:T:TA	donor_gain	1.0000
19:43797826:TTGC:T	acceptor_gain	0.9900
19:43797830:C:CA	acceptor_loss	0.9900
19:43798454:CCA:C	donor_gain	0.9900
19:43798474:G:A	donor_gain	0.9900

AlphaMissense

1614 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:43798481:A:C	F164C	0.998
19:43798505:C:G	C156S	0.997
19:43798506:A:T	C156S	0.997
19:43798855:G:C	N109K	0.996
19:43798855:G:T	N109K	0.996
19:43798480:G:C	F164L	0.995
19:43798480:G:T	F164L	0.995
19:43798482:A:G	F164L	0.995
19:43798568:C:G	C135S	0.995
19:43798569:A:T	C135S	0.995
19:43797796:C:T	C184Y	0.994
19:43797796:C:G	C184S	0.993
19:43797797:A:T	C184S	0.993
19:43798476:C:A	G166C	0.993
19:43798506:A:G	C156R	0.993
19:43798859:C:G	C108S	0.993
19:43798860:A:T	C108S	0.993
19:43797734:C:A	G205C	0.992
19:43797753:C:A	W198C	0.992
19:43797753:C:G	W198C	0.992
19:43798535:C:G	C146S	0.992
19:43798536:A:T	C146S	0.992
19:43798874:C:G	C103S	0.992
19:43798875:A:T	C103S	0.992
19:43798484:C:G	C163S	0.991
19:43798485:A:T	C163S	0.991
19:43798504:A:C	C156W	0.991
19:43798569:A:G	C135R	0.991
19:43798957:C:A	K75N	0.991
19:43798957:C:G	K75N	0.991

dbSNP variants (sampled 300 via entrez): RS1000258241 (19:43812217 T>C), RS1000351866 (19:43805668 T>C), RS1000465405 (19:43799210 T>G), RS1000487397 (19:43811506 C>A,T), RS1000626487 (19:43799630 C>T), RS1000671526 (19:43805751 A>C,G), RS1000893757 (19:43798788 G>T), RS1001064246 (19:43818177 G>A), RS1001173416 (19:43814444 T>G), RS1001242713 (19:43806209 C>T), RS1001276016 (19:43810382 G>A), RS1001354372 (19:43812426 A>C,G), RS1001427866 (19:43812788 A>G), RS1001433376 (19:43814840 G>A,T), RS1001528935 (19:43801360 G>A)

Disease associations

OMIM: gene MIM:619618 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001937_27	Breast cancer	2.000000e-10
GCST002522_1	Reading or mathematical ability	8.000000e-09
GCST004988_14	Breast cancer	1.000000e-16

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005229	reading

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
sodium arsenate	increases abundance, decreases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
benzo(e)pyrene	increases methylation	1
hydroquinone	increases expression	1
CGP 52608	increases reaction, affects binding	1
abrine	increases expression	1
bisphenol S	decreases methylation	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Calcitriol	increases expression	1
Methapyrilene	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
Cadmium Chloride	increases expression	1
Okadaic Acid	increases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

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