LNP1

Summary

LNP1 (leukemia NUP98 fusion partner 1, HGNC:28014) is a protein-coding gene on chromosome 3q12.2, encoding Leukemia NUP98 fusion partner 1 (A1A4G5).

At a glance

• Clinical variants (ClinVar): 29 total
• MANE Select transcript: NM_001085451

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28014
Approved symbol	LNP1
Name	leukemia NUP98 fusion partner 1
Location	3q12.2
Locus type	gene with protein product
Status	Approved
Aliases	NP3
Ensembl gene	ENSG00000206535
Ensembl biotype	protein_coding
Entrez	348801

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 nonsense_mediated_decay

ENST00000383693, ENST00000466996, ENST00000489752, ENST00000884269, ENST00000884270, ENST00000884271, ENST00000884272, ENST00000941632

RefSeq mRNA: 1 — MANE Select: NM_001085451 NM_001085451

CCDS: CCDS43120

Canonical transcript exons

ENST00000383693 — 4 exons

Exon	Start	End
ENSE00001498156	100455777	100456319
ENSE00001498157	100451719	100451949
ENSE00001498158	100429697	100429885
ENSE00001498159	100401539	100402439

Expression profiles

Bgee: expression breadth ubiquitous, 219 present calls, max score 94.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.5410 / max 102.7830, expressed in 1373 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
37607	4.2581	1359
37610	0.1369	43
37609	0.0762	6
37608	0.0699	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cardiac muscle of right atrium	UBERON:0003379	94.73	silver quality
sperm	CL:0000019	92.30	gold quality
pancreatic ductal cell	CL:0002079	90.18	silver quality
tibialis anterior	UBERON:0001385	87.05	silver quality
adult organism	UBERON:0007023	86.40	gold quality
myocardium	UBERON:0002349	86.11	silver quality
left testis	UBERON:0004533	85.54	gold quality
endothelial cell	CL:0000115	85.50	gold quality
testis	UBERON:0000473	85.37	gold quality
kidney epithelium	UBERON:0004819	85.08	gold quality
middle temporal gyrus	UBERON:0002771	84.89	gold quality
oviduct epithelium	UBERON:0004804	84.54	gold quality
saphenous vein	UBERON:0007318	84.46	gold quality
right testis	UBERON:0004534	84.45	gold quality
vena cava	UBERON:0004087	83.47	gold quality
prefrontal cortex	UBERON:0000451	82.69	gold quality
deltoid	UBERON:0001476	82.43	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.10	gold quality
nucleus accumbens	UBERON:0001882	82.02	gold quality
Brodmann (1909) area 23	UBERON:0013554	81.97	gold quality
putamen	UBERON:0001874	81.38	gold quality
entorhinal cortex	UBERON:0002728	81.35	gold quality
frontal cortex	UBERON:0001870	81.15	gold quality
right coronary artery	UBERON:0001625	81.11	gold quality
quadriceps femoris	UBERON:0001377	80.76	silver quality
neocortex	UBERON:0001950	80.68	gold quality
superior frontal gyrus	UBERON:0002661	80.50	gold quality
caudate nucleus	UBERON:0001873	80.46	gold quality
postcentral gyrus	UBERON:0002581	80.44	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.35	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-137537	yes	5.38
E-ANND-3	no	2.68

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting LNP1, 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-4283	100.00	66.42	2097
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-4489	99.50	65.56	785
HSA-MIR-4426	99.17	66.74	1949
HSA-MIR-6770-5P	98.97	66.76	1853
HSA-MIR-3154	98.94	66.55	1455
HSA-MIR-219A-1-3P	98.91	67.87	639
HSA-MIR-4260	98.78	65.37	848
HSA-MIR-5572	98.55	65.84	970
HSA-MIR-1322	97.98	68.96	625
HSA-MIR-127-5P	97.78	67.64	869
HSA-MIR-4724-3P	97.57	67.31	785
HSA-MIR-4793-5P	96.88	65.90	872

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lnp1	ENSMUSG00000109588
rattus_norvegicus	Lnp1	ENSRNOG00000039649

Protein

Protein identifiers

Leukemia NUP98 fusion partner 1 — A1A4G5 (reviewed: A1A4G5)

All UniProt accessions (3): A1A4G5, C9J587, F8WF60

UniProt curated annotations — full annotation on UniProt →

Disease relevance. A chromosomal aberration involving LNP1 is found in a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(3;11)(q12.2;p15.4) with NUP98.

RefSeq proteins (1): NP_001078920* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029280	LNP1	Family

Pfam: PF15419

UniProt features (6 total): region of interest 3, compositionally biased region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A1A4G5-F1	64.30	0.04

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 26 (showing top): MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP, chr3q12, KOYAMA_SEMA3B_TARGETS_DN, WHITFIELD_CELL_CYCLE_M_G1, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, ATF6_TARGET_GENES, DLX4_TARGET_GENES, ELF2_TARGET_GENES, KLF7_TARGET_GENES, MAFG_TARGET_GENES, ZFP3_TARGET_GENES, ZNF350_TARGET_GENES, ZNF513_TARGET_GENES, ZNF618_TARGET_GENES, MIR4283

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

462 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LNP1	PRTN3	P15637	809
LNP1	MT-CO2	P00403	767
LNP1	MRGPRD	Q8TDS7	570
LNP1	URB1	O60287	487
LNP1	ANOS1	P23352	464
LNP1	IL31RA	Q8NI17	454
LNP1	MT-CO3	P00414	437
LNP1	NDUFB11	Q9NX14	436
LNP1	EXOC1L	A0A1B0GW35	397
LNP1	SPP1	P10451	369
LNP1	MT-CO1	P00395	368
LNP1	MRGPRX1	Q96LB2	359
LNP1	TAGLN3	Q9UI15	359
LNP1	CPZ	Q66K79	357
LNP1	NPC1	O15118	326
LNP1	OSMR	Q99650	326

IntAct

7 interactions, top by confidence:

A	B	Type	Score
	LNP1	psi-mi:“MI:0915”(physical association)	0.560
LNP1	GAPDH	psi-mi:“MI:0915”(physical association)	0.400
LNP1	GLUL	psi-mi:“MI:0914”(association)	0.350
LNP1		psi-mi:“MI:0915”(physical association)	0.000

BioGRID (25): LNP1 (Affinity Capture-Western), LNP1 (Affinity Capture-Western), LNP1 (Affinity Capture-Western), LNP1 (Affinity Capture-Western), LNP1 (Affinity Capture-Western), LNP1 (Affinity Capture-Western), LNP1 (Two-hybrid), GAPDH (Proximity Label-MS), LNP1 (Affinity Capture-RNA), AHCYL2 (Affinity Capture-MS), YWHAE (Affinity Capture-MS), YWHAH (Affinity Capture-MS), YWHAG (Affinity Capture-MS), YWHAZ (Affinity Capture-MS), GLUL (Affinity Capture-MS)

ESM2 similar proteins: A0A140LFM6, A0A1B0GVH6, A1A4G5, A1CQN6, A7A241, A9RNY0, B0QZF7, B9UYK6, E9Q309, H0WFA5, O23372, O35413, O94875, P02686, P43587, Q0VFP3, Q0WL69, Q12912, Q17QQ9, Q1G3K8, Q32KY7, Q3UTJ2, Q499E5, Q4R309, Q4R881, Q4V7T5, Q56WM6, Q5E9A0, Q5PPL1, Q5R6I3, Q5VT06, Q62417, Q6AYU0, Q6DD19, Q6GP48, Q6H7U2, Q8K2H1, Q8L4M6, Q8NEY8, Q8NG27

Diamond homologs: A1A4G5, Q4R881

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	22
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1178 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:100429779:T:C	M17T	0.994
3:100429766:T:C	F13L	0.993
3:100429768:T:A	F13L	0.993
3:100429768:T:G	F13L	0.993
3:100429777:G:C	W16C	0.993
3:100429777:G:T	W16C	0.993
3:100429775:T:A	W16R	0.992
3:100429775:T:C	W16R	0.992
3:100429780:G:A	M17I	0.989
3:100429780:G:C	M17I	0.989
3:100429780:G:T	M17I	0.989
3:100429787:T:C	F20L	0.989
3:100429789:C:A	F20L	0.989
3:100429789:C:G	F20L	0.989
3:100429781:A:C	S18R	0.988
3:100429783:C:A	S18R	0.988
3:100429783:C:G	S18R	0.988
3:100429792:G:C	W21C	0.988
3:100429792:G:T	W21C	0.988
3:100429784:A:C	S19R	0.986
3:100429786:C:A	S19R	0.986
3:100429786:C:G	S19R	0.986
3:100429790:T:A	W21R	0.982
3:100429790:T:C	W21R	0.982
3:100429767:T:C	F13S	0.980
3:100429767:T:G	F13C	0.976
3:100429770:C:A	A14D	0.975
3:100429793:G:C	G22R	0.975
3:100429776:G:C	W16S	0.973
3:100429782:G:T	S18I	0.964

dbSNP variants (sampled 300 via entrez): RS1000095939 (3:100434807 G>A), RS1000150043 (3:100409057 G>A), RS1000166356 (3:100421439 C>A,T), RS1000269038 (3:100426762 C>T), RS1000315594 (3:100447036 G>A,T), RS1000454284 (3:100432996 A>G), RS1000482856 (3:100408945 T>C), RS1000521171 (3:100400805 G>A), RS1000524664 (3:100454808 C>G), RS1000575626 (3:100433299 G>A,C), RS1000622918 (3:100421028 G>A,C,T), RS1000632607 (3:100427144 C>G,T), RS1000915140 (3:100440316 C>A), RS1000976708 (3:100439976 G>A), RS1000997032 (3:100425988 G>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:618090

GenCC curated gene-disease

Mondo (1): neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum (MONDO:0060761)

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
Valproic Acid	affects expression, increases expression	2
FR900359	decreases phosphorylation	1
2-methyl-4-isothiazolin-3-one	increases expression	1
abrine	decreases expression	1
Sunitinib	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	decreases expression	1
Diethylhexyl Phthalate	increases expression	1
Estradiol	affects expression	1
Nickel	decreases expression	1
Quercetin	increases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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