KPLCE

Summary

KPLCE (KPRP N-terminal and LCE C-terminal like protein, HGNC:29468) is a protein-coding gene on chromosome 1q21.3, encoding Protein KPLCE (Q5T750).

Predicted to be involved in epidermis development.

Source: NCBI Gene 100129271 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_001024679

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29468
Approved symbol	KPLCE
Name	KPRP N-terminal and LCE C-terminal like protein
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Aliases	LEP7, XP32
Ensembl gene	ENSG00000198854
Ensembl biotype	protein_coding
Entrez	100129271

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000368775

RefSeq mRNA: 1 — MANE Select: NM_001024679 NM_001024679

CCDS: CCDS44226

Canonical transcript exons

ENST00000368775 — 1 exons

Exon	Start	End
ENSE00001447937	152719522	152720470

Expression profiles

Bgee: expression breadth ubiquitous, 123 present calls, max score 97.86.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of leg	UBERON:0001511	97.86	gold quality
skin of abdomen	UBERON:0001416	97.32	gold quality
zone of skin	UBERON:0000014	96.50	gold quality
upper arm skin	UBERON:0004263	96.49	gold quality
upper leg skin	UBERON:0004262	92.80	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.42	gold quality
skin of hip	UBERON:0001554	87.15	gold quality
endometrium epithelium	UBERON:0004811	76.07	gold quality
nipple	UBERON:0002030	73.46	gold quality
type B pancreatic cell	CL:0000169	70.22	gold quality
Brodmann (1909) area 10	UBERON:0013541	68.93	gold quality
olfactory bulb	UBERON:0002264	66.30	gold quality
triceps brachii	UBERON:0001509	64.67	gold quality
gluteal muscle	UBERON:0002000	64.47	gold quality
frontal pole	UBERON:0002795	63.13	gold quality
middle frontal gyrus	UBERON:0002702	63.02	gold quality
paraflocculus	UBERON:0005351	62.71	gold quality
hair follicle	UBERON:0002073	60.95	gold quality
cerebellar vermis	UBERON:0004720	59.91	gold quality
secondary oocyte	CL:0000655	58.68	gold quality
penis	UBERON:0000989	56.72	silver quality
quadriceps femoris	UBERON:0001377	56.03	gold quality
thymus	UBERON:0002370	55.13	gold quality
vastus lateralis	UBERON:0001379	54.81	gold quality
myocardium	UBERON:0002349	54.80	gold quality
lower esophagus mucosa	UBERON:0035834	54.09	gold quality
seminal vesicle	UBERON:0000998	53.45	gold quality
gastrocnemius	UBERON:0001388	52.68	gold quality
tibia	UBERON:0000979	51.52	gold quality
nasal cavity epithelium	UBERON:0005384	51.41	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting KPLCE, 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-7150	99.62	66.80	1322
HSA-MIR-516B-5P	99.56	66.33	1495
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4312	99.34	67.30	511
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-4451	98.82	68.17	1455
HSA-MIR-6882-3P	98.23	67.01	1119
HSA-MIR-4736	97.96	65.89	1287
HSA-MIR-3936	97.64	64.47	732

Literature-anchored findings (GeneRIF, showing 1)

• SNPs in C1orf68 are associated with increased risk of candidemia. (PMID:25197941)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Kplce	ENSMUSG00000090314
rattus_norvegicus	Kplce	ENSRNOG00000023511

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), PRR9 (ENSG00000203783), LELP1 (ENSG00000203784), LCE1F (ENSG00000240386), LCE3C (ENSG00000244057)

Protein

Protein identifiers

Protein KPLCE — Q5T750 (reviewed: Q5T750)

Alternative names: KPRP N-terminal and LCE C-terminal-like protein, Skin-specific protein 32

All UniProt accessions (1): Q5T750

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Skin-specific.

RefSeq proteins (1): NP_001019850* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR053348	KPLCE	Family

UniProt features (6 total): sequence variant 3, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T750-F1	45.70	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): MAHAJAN_RESPONSE_TO_IL1A_DN, GOBP_EPIDERMIS_DEVELOPMENT, chr1q21, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, KRAS.600.LUNG.BREAST_UP.V1_UP, KRAS.PROSTATE_UP.V1_DN, MIR516B_5P, MIR6882_3P, GSE13306_TREG_VS_TCONV_LAMINA_PROPRIA_UP, GSE13306_RA_VS_UNTREATED_TCONV_DN, MIR4312, NAKAYA_PLASMACYTOID_DENDRITIC_CELL_FLUMIST_AGE_18_50YO_7DY_DN, GSE20715_WT_VS_TLR4_KO_6H_OZONE_LUNG_DN, GSE27786_NKTCELL_VS_MONO_MAC_DN, GSE29618_PRE_VS_DAY7_FLU_VACCINE_PDC_UP

GO Biological Process (1): epidermis development (GO:0008544)

GO Molecular Function (0):

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
tissue development	1

Protein interactions and networks

STRING

306 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KPLCE	LCE4A	Q5TA78	767
KPLCE	CRCT1	Q9UGL9	555
KPLCE	TAGAP	Q8N103	542
KPLCE	KPRP	Q5T749	498
KPLCE	LELP1	Q5T871	495
KPLCE	PRR9	Q5T870	491
KPLCE	SAXO5	Q8NA69	445
KPLCE	CD58	P19256	376
KPLCE	LCE2B	O14633	338
KPLCE	SPRR4	Q96PI1	323
KPLCE	LCE1A	Q5T7P2	323
KPLCE	SPRR3	Q9UBC9	321
KPLCE	PGLYRP4	Q96LB8	308
KPLCE	LCE2A	Q5TA79	308
KPLCE	LORICRIN	P23490	305

IntAct

25 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
Retreg2		psi-mi:“MI:0915”(physical association)	0.400
		psi-mi:“MI:0914”(association)	0.350
METTL3	TUBAL3	psi-mi:“MI:0914”(association)	0.350
WTAP	DDX39A	psi-mi:“MI:0914”(association)	0.350
METTL14	HMGB1P1	psi-mi:“MI:0914”(association)	0.350
LRRK2		psi-mi:“MI:0914”(association)	0.350
	AP3B1	psi-mi:“MI:0914”(association)	0.350
NELFE	H1-2	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
ATG16L1		psi-mi:“MI:0914”(association)	0.350
SF3B1	RBM10	psi-mi:“MI:0914”(association)	0.350
ARMC9	PRMT5	psi-mi:“MI:0914”(association)	0.350
FHIP2A	MED19	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (65): C1orf68 (Affinity Capture-MS), C1orf68 (Affinity Capture-MS), C1orf68 (Affinity Capture-MS), C1orf68 (Affinity Capture-MS), C1orf68 (Affinity Capture-MS), C1orf68 (Affinity Capture-MS), C1orf68 (Affinity Capture-MS), C1orf68 (Affinity Capture-MS), C1orf68 (Affinity Capture-MS), C1orf68 (Affinity Capture-MS), C1orf68 (Affinity Capture-MS), C1orf68 (Affinity Capture-MS), C1orf68 (Affinity Capture-MS), SERPINB12 (Affinity Capture-MS), ANXA2 (Affinity Capture-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 24 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
Processing of Capped Intron-Containing Pre-mRNA	5	22.8×	3e-04

GO biological processes:

GO term	Partners	Fold	FDR
mRNA splicing, via spliceosome	5	24.1×	2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	5
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

173 predictions. Top by Δscore:

Variant	Effect	Δscore
1:152719917:C:G	donor_gain	0.9900
1:152719927:G:GT	donor_gain	0.9700
1:152719917:C:CG	donor_gain	0.9600
1:152719911:G:GT	donor_gain	0.9500
1:152719926:GG:G	donor_gain	0.9500
1:152719787:TG:T	donor_gain	0.9400
1:152719911:GAC:G	donor_gain	0.9400
1:152719850:TG:T	donor_gain	0.9100
1:152719851:G:GT	donor_gain	0.9000
1:152719914:GTGC:G	donor_gain	0.8900
1:152719915:TGCT:T	donor_gain	0.8900
1:152719788:G:GT	donor_gain	0.8800
1:152719947:C:G	donor_gain	0.8700
1:152719567:AAAG:A	donor_gain	0.8500
1:152719818:T:G	donor_gain	0.8400
1:152719788:GA:G	donor_gain	0.8300
1:152719789:AA:A	donor_gain	0.8300
1:152719749:GACC:G	donor_gain	0.8200
1:152719916:GC:G	donor_gain	0.8100
1:152719913:C:G	donor_gain	0.7900
1:152720026:A:AG	acceptor_gain	0.7400
1:152720027:G:GG	acceptor_gain	0.7400
1:152719928:G:T	donor_gain	0.7200
1:152719815:C:CG	donor_gain	0.7100
1:152720027:GCTA:G	acceptor_gain	0.7100
1:152720027:GCT:G	acceptor_gain	0.7000
1:152719873:A:G	donor_gain	0.6900
1:152719931:C:CG	donor_gain	0.6800
1:152719932:T:G	donor_gain	0.6800
1:152719851:GA:G	donor_gain	0.6700

AlphaMissense

1607 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:152720053:T:C	F178L	0.988
1:152720055:C:A	F178L	0.988
1:152720055:C:G	F178L	0.988
1:152720213:T:C	I231T	0.984
1:152720077:T:A	W186R	0.982
1:152720077:T:C	W186R	0.982
1:152720079:G:C	W186C	0.979
1:152720079:G:T	W186C	0.979
1:152720216:T:C	I232T	0.971
1:152720073:A:C	R184S	0.964
1:152720073:A:T	R184S	0.964
1:152720209:G:A	G230R	0.963
1:152720209:G:C	G230R	0.963
1:152720213:T:G	I231S	0.963
1:152720223:G:A	M234I	0.951
1:152720223:G:C	M234I	0.951
1:152720223:G:T	M234I	0.951
1:152720210:G:T	G230V	0.949
1:152720216:T:G	I232S	0.949
1:152720233:G:C	G238R	0.948
1:152720072:G:C	R184T	0.947
1:152720213:T:A	I231N	0.947
1:152720216:T:A	I232N	0.940
1:152720242:T:C	C241R	0.939
1:152720026:A:C	S169R	0.933
1:152720028:C:A	S169R	0.933
1:152720028:C:G	S169R	0.933
1:152720210:G:A	G230E	0.932
1:152720072:G:T	R184I	0.931
1:152720074:C:A	R185S	0.931

dbSNP variants (sampled 300 via entrez): RS1000090998 (1:152719676 C>G,T), RS1000523367 (1:152719421 A>G), RS1002215238 (1:152719970 G>A), RS1002244634 (1:152719737 T>A), RS1003910070 (1:152719352 T>C), RS1005900203 (1:152718609 C>T), RS1005931504 (1:152718447 T>C), RS1006253656 (1:152717901 G>A,T), RS1007086870 (1:152718107 G>A), RS1008409086 (1:152719867 T>A,C), RS1009566350 (1:152719923 C>A,G,T), RS1010333700 (1:152718664 G>A), RS1013282668 (1:152718400 A>G), RS1013667902 (1:152718582 G>C), RS1014358249 (1:152718724 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

5 associations (top):

Study	Trait	p-value
GCST007563_33	Allergic disease (asthma, hay fever or eczema)	3.000000e-11
GCST007564_24	Asthma or allergic disease (pleiotropy)	5.000000e-12
GCST008479_3	Psoriasis	6.000000e-11
GCST008916_82	Asthma	5.000000e-27
GCST008916_92	Asthma	6.000000e-16

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenate	increases abundance, decreases expression	1
sodium arsenite	affects expression	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Aflatoxin B1	decreases methylation	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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