LELP1

Summary

LELP1 (late cornified envelope like proline rich 1, HGNC:32046) is a protein-coding gene on chromosome 1q21.3, encoding Late cornified envelope-like proline-rich protein 1 (Q5T871).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 16 total
• MANE Select transcript: NM_001010857

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32046
Approved symbol	LELP1
Name	late cornified envelope like proline rich 1
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000203784
Ensembl biotype	protein_coding
OMIM	611042
Entrez	149018

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000368747

RefSeq mRNA: 1 — MANE Select: NM_001010857 NM_001010857

CCDS: CCDS30869

Canonical transcript exons

ENST00000368747 — 2 exons

Exon	Start	End
ENSE00001447890	153204687	153205120
ENSE00001447891	153203430	153203531

Expression profiles

Bgee: expression breadth ubiquitous, 125 present calls, max score 99.64.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.0552 / max 917.9282, expressed in 5 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5375	1.0281	5
5377	0.0077	2
5376	0.0072	2
5378	0.0063	2
5379	0.0037	2
201738	0.0023	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	99.64	gold quality
right testis	UBERON:0004534	99.14	gold quality
left testis	UBERON:0004533	99.12	gold quality
adult organism	UBERON:0007023	97.80	gold quality
testis	UBERON:0000473	96.30	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	95.05	gold quality
buccal mucosa cell	CL:0002336	85.46	silver quality
kidney epithelium	UBERON:0004819	84.29	gold quality
cerebellar vermis	UBERON:0004720	78.12	gold quality
tendon of biceps brachii	UBERON:0008188	73.91	silver quality
nasal cavity epithelium	UBERON:0005384	73.01	gold quality
upper arm skin	UBERON:0004263	72.53	gold quality
myocardium	UBERON:0002349	70.51	gold quality
cardia of stomach	UBERON:0001162	70.45	gold quality
pharyngeal mucosa	UBERON:0000355	70.28	gold quality
substantia nigra pars reticulata	UBERON:0001966	70.08	gold quality
vena cava	UBERON:0004087	70.01	gold quality
inferior vagus X ganglion	UBERON:0005363	69.92	gold quality
ventral tegmental area	UBERON:0002691	69.91	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	69.91	gold quality
nipple	UBERON:0002030	69.66	gold quality
superior surface of tongue	UBERON:0007371	69.62	gold quality
cardiac muscle of right atrium	UBERON:0003379	69.61	gold quality
body of tongue	UBERON:0011876	69.60	gold quality
tongue	UBERON:0001723	69.51	gold quality
pericardium	UBERON:0002407	69.51	gold quality
left ventricle myocardium	UBERON:0006566	69.49	gold quality
epithelial cell of pancreas	CL:0000083	69.47	gold quality
lateral nuclear group of thalamus	UBERON:0002736	69.44	gold quality
pons	UBERON:0000988	69.42	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	8439.72
E-ANND-3	no	0.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

19 targeting LELP1, 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-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-584-3P	99.35	67.69	1082
HSA-MIR-4758-3P	99.12	63.96	869
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-4277	98.34	67.17	1323
HSA-MIR-6880-5P	98.08	65.59	1282
HSA-MIR-3928-3P	97.61	66.53	1096
HSA-MIR-431-5P	96.16	66.50	652
HSA-MIR-6815-5P	96.05	65.55	662
HSA-MIR-6865-5P	96.05	65.58	675

Literature-anchored findings (GeneRIF, showing 2)

• Suggest that rs7534334 SNP, located in the LELP1 region, may be a potential genetic marker for the risk and course of atopic dermatitis. (PMID:26608070)
• mRNA levels of LELP1, SPRR1Av1, and SPRR1Av2 were significantly higher in the skin of patients with AD compared with the control group. (PMID:27304082)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lelp1	ENSMUSG00000027927

Paralogs (20): LCE2B (ENSG00000159455), SPRR2G (ENSG00000159516), LCE3D (ENSG00000163202), SPRR3 (ENSG00000163209), SPRR1B (ENSG00000169469), SPRR1A (ENSG00000169474), LCE1D (ENSG00000172155), SPRR4 (ENSG00000184148), LCE3A (ENSG00000185962), LCE3E (ENSG00000185966), LCE5A (ENSG00000186207), LCE1E (ENSG00000186226), LCE2A (ENSG00000187173), LCE2C (ENSG00000187180), LCE2D (ENSG00000187223), LCE3B (ENSG00000187238), KPLCE (ENSG00000198854), PRR9 (ENSG00000203783), LCE1F (ENSG00000240386), LCE3C (ENSG00000244057)

Protein

Protein identifiers

Late cornified envelope-like proline-rich protein 1 — Q5T871 (reviewed: Q5T871)

Alternative names: Novel small proline-rich protein

All UniProt accessions (1): Q5T871

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the cornifin (SPRR) family.

RefSeq proteins (1): NP_001010857* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026076	Lelp1	Family

Pfam: PF15042

UniProt features (2 total): chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T871-F1	68.31	0.00

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-6809371	Formation of the cornified envelope
R-HSA-1266738	Developmental Biology
R-HSA-6805567	Keratinization

MSigDB gene sets: 32 (showing top): chr1q21, MYC_UP.V1_UP, SRC_UP.V1_UP, REACTOME_KERATINIZATION, REACTOME_FORMATION_OF_THE_CORNIFIED_ENVELOPE, GSE13522_WT_VS_IFNG_KO_SKING_T_CRUZI_Y_STRAIN_INF_UP, GSE13522_WT_VS_IFNG_KO_SKING_T_CRUZI_Y_STRAIN_INF_DN, MIR92A_2_5P, MIR223_3P, GSE13306_TREG_VS_TCONV_DN, GSE9946_IMMATURE_VS_MATURE_STIMULATORY_DC_DN, GSE9946_MATURE_STIMULATORY_VS_LISTERIA_INF_MATURE_DC_DN, GSE9946_LISTERIA_INF_MATURE_VS_PROSTAGLANDINE2_TREATED_MATURE_DC_DN, GSE12707_AT16L1_HYPOMORPH_VS_WT_THYMUS_UP, GSE32423_IL7_VS_IL7_IL4_MEMORY_CD8_TCELL_DN

GO Biological Process (0):

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

GO Cellular Component (0):

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Keratinization	1
Developmental Biology	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

614 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LELP1	KPRP	Q5T749	607
LELP1	SPRR4	Q96PI1	604
LELP1	TCHHL1	Q5QJ38	601
LELP1	LRCOL1	A6NCL2	582
LELP1	PRR9	Q5T870	574
LELP1	KPLCE	Q5T750	495
LELP1	SPMIP4	Q8N865	479
LELP1	CRCT1	Q9UGL9	474
LELP1	S100A2	P29034	469
LELP1	CETN1	Q12798	467
LELP1	H1-7	Q75WM6	465
LELP1	SPRR3	Q9UBC9	464
LELP1	FAM229B	Q4G0N7	462
LELP1	SPRR2A	P35326	461
LELP1	S100A3	P33764	423

IntAct

44 interactions, top by confidence:

A	B	Type	Score
KRTAP5-2	LELP1	psi-mi:“MI:0915”(physical association)	0.560
ALPP	LELP1	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-8	LELP1	psi-mi:“MI:0915”(physical association)	0.560
LELP1	KRTAP5-3	psi-mi:“MI:0915”(physical association)	0.560
KRTAP5-9	LELP1	psi-mi:“MI:0915”(physical association)	0.560
CLIC3	LELP1	psi-mi:“MI:0915”(physical association)	0.560
LELP1	KRTAP5-2	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-5	LELP1	psi-mi:“MI:0915”(physical association)	0.560
LELP1	KRTAP4-12	psi-mi:“MI:0915”(physical association)	0.560
LELP1	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.560
LELP1	KRTAP4-11	psi-mi:“MI:0915”(physical association)	0.560
LELP1	KRTAP4-5	psi-mi:“MI:0915”(physical association)	0.560
LELP1	SLC39A7	psi-mi:“MI:0915”(physical association)	0.560
LELP1	KRTAP5-11	psi-mi:“MI:0915”(physical association)	0.560
LELP1	KRTAP5-6	psi-mi:“MI:0915”(physical association)	0.560
LELP1	FADS2	psi-mi:“MI:0915”(physical association)	0.400
KRTAP5-3	LELP1	psi-mi:“MI:0915”(physical association)	0.000
LELP1	KRTAP5-9	psi-mi:“MI:0915”(physical association)	0.000
CLIC3	LELP1	psi-mi:“MI:0915”(physical association)	0.000
KRTAP10-5	LELP1	psi-mi:“MI:0915”(physical association)	0.000
KRTAP4-12	LELP1	psi-mi:“MI:0915”(physical association)	0.000
KRTAP9-2	LELP1	psi-mi:“MI:0915”(physical association)	0.000
KRTAP4-11	LELP1	psi-mi:“MI:0915”(physical association)	0.000
KRTAP4-5	LELP1	psi-mi:“MI:0915”(physical association)	0.000
KRTAP5-6	LELP1	psi-mi:“MI:0915”(physical association)	0.000
ALPP	LELP1	psi-mi:“MI:0915”(physical association)	0.000
KRTAP10-8	LELP1	psi-mi:“MI:0915”(physical association)	0.000
KRTAP5-9	LELP1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): LELP1 (Two-hybrid), LELP1 (Two-hybrid), LELP1 (Two-hybrid), LELP1 (Two-hybrid), LELP1 (Two-hybrid), LELP1 (Two-hybrid), KRTAP5-11 (Two-hybrid), KRTAP5-6 (Two-hybrid), KRTAP5-2 (Two-hybrid), KRTAP4-11 (Two-hybrid), KRTAP4-12 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP10-5 (Two-hybrid), KRTAP5-9 (Two-hybrid), LELP1 (Proximity Label-MS)

ESM2 similar proteins: A0A1B0GTR4, A6QNZ4, O14633, O70554, O70555, O70556, O70557, O70558, O70559, O70560, O70562, P15265, P22528, P22531, P22532, P35321, P35322, P35323, P35324, P35325, P35326, P49901, Q28658, Q32L04, Q4KL71, Q4R956, Q5T5B0, Q5T750, Q5T752, Q5T754, Q5T870, Q5T871, Q5TA76, Q5TA77, Q5TA78, Q5TA79, Q5TA81, Q5TA82, Q5TCM9, Q62266

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 15 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	10	42.9×	8e-15

Disease & clinical

Clinical variants and AI predictions

ClinVar

16 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

52 predictions. Top by Δscore:

Variant	Effect	Δscore
1:153203529:GGG:G	donor_gain	1.0000
1:153203530:GGG:G	donor_gain	1.0000
1:153204684:CAGG:C	acceptor_loss	1.0000
1:153204685:A:AG	acceptor_gain	1.0000
1:153204685:AG:A	acceptor_gain	1.0000
1:153204685:AGGGC:A	acceptor_loss	1.0000
1:153204686:G:GT	acceptor_gain	1.0000
1:153204686:GG:G	acceptor_gain	1.0000
1:153203527:GAGGG:G	donor_gain	0.9900
1:153203528:AGGG:A	donor_gain	0.9900
1:153203528:AGGGG:A	donor_loss	0.9900
1:153203529:GGGG:G	donor_gain	0.9900
1:153203530:GG:G	donor_gain	0.9900
1:153203531:GG:G	donor_gain	0.9900
1:153203531:GGTAA:G	donor_loss	0.9900
1:153203532:G:GG	donor_gain	0.9900
1:153203532:GT:G	donor_loss	0.9900
1:153203533:TAAGT:T	donor_loss	0.9900
1:153204682:T:TA	acceptor_gain	0.9900
1:153204685:AGG:A	acceptor_gain	0.9900
1:153204686:GGG:G	acceptor_gain	0.9900
1:153204686:GGGC:G	acceptor_gain	0.9900
1:153204686:GGGCT:G	acceptor_gain	0.9900
1:153204684:CAGGG:C	acceptor_gain	0.9700
1:153204685:AGGG:A	acceptor_gain	0.9700
1:153203534:AAGTT:A	donor_loss	0.9500
1:153204108:GGAT:G	donor_gain	0.9200
1:153204682:TGCAG:T	acceptor_gain	0.9200
1:153204683:GCAGG:G	acceptor_gain	0.9200
1:153204686:G:T	acceptor_gain	0.9000

AlphaMissense

635 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:153204798:T:A	C31S	0.931
1:153204799:G:C	C31S	0.931
1:153204798:T:C	C31R	0.928
1:153204823:T:C	L39P	0.911
1:153204814:T:C	L36S	0.909
1:153204774:T:A	C23S	0.886
1:153204775:G:C	C23S	0.886
1:153204774:T:C	C23R	0.885
1:153204834:T:C	C43R	0.880
1:153204800:C:G	C31W	0.879
1:153204826:T:C	L40P	0.875
1:153204836:T:G	C43W	0.859
1:153204834:T:A	C43S	0.857
1:153204835:G:C	C43S	0.857
1:153204786:T:C	C27R	0.842
1:153204807:A:C	S34R	0.837
1:153204809:C:A	S34R	0.837
1:153204809:C:G	S34R	0.837
1:153204786:T:A	C27S	0.836
1:153204787:G:C	C27S	0.836
1:153204810:T:C	C35R	0.835
1:153204776:T:G	C23W	0.822
1:153204821:G:C	K38N	0.794
1:153204821:G:T	K38N	0.794
1:153204799:G:A	C31Y	0.790
1:153204810:T:A	C35S	0.788
1:153204811:G:C	C35S	0.788
1:153204799:G:T	C31F	0.775
1:153204775:G:T	C23F	0.773
1:153204798:T:G	C31G	0.769

dbSNP variants (sampled 300 via entrez): RS1001480205 (1:153205495 G>A), RS1003243020 (1:153201985 A>G), RS1004179690 (1:153205334 CAAA>C), RS1004813800 (1:153202671 G>A), RS1004920422 (1:153204414 G>A,T), RS1005169841 (1:153202412 C>T), RS1005210759 (1:153203957 T>C,G), RS1006433846 (1:153203896 A>G), RS1006896706 (1:153204214 A>C,G,T), RS1006994641 (1:153203178 T>G), RS1007335703 (1:153204557 G>A,T), RS1007757126 (1:153204792 T>C), RS1008768705 (1:153204754 C>G,T), RS1008851357 (1:153203160 G>A), RS1009068755 (1:153204486 G>A)

Disease associations

OMIM: gene MIM:611042 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008916_87	Asthma	2.000000e-13

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Am 580	decreases expression	1
CGP 52608	affects binding, increases reaction	1
Rosiglitazone	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Amiodarone	increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Malathion	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Lactic Acid	increases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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