NXPE1

Summary

NXPE1 (neurexophilin and PC-esterase domain family member 1, HGNC:28527) is a protein-coding gene on chromosome 11q23.2, encoding NXPE family member 1 (Q8N323).

Predicted to be located in extracellular region and membrane.

Source: NCBI Gene 120400 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 74 total
• MANE Select transcript: NM_001395504

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28527
Approved symbol	NXPE1
Name	neurexophilin and PC-esterase domain family member 1
Location	11q23.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC34290
Ensembl gene	ENSG00000095110
Ensembl biotype	protein_coding
Entrez	120400

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 9 protein_coding, 1 retained_intron

ENST00000251921, ENST00000534921, ENST00000536271, ENST00000536312, ENST00000539878, ENST00000696071, ENST00000867473, ENST00000867474, ENST00000867475, ENST00000867476

RefSeq mRNA: 3 — MANE Select: NM_001395504 NM_001367953, NM_001395504, NM_152315

CCDS: CCDS8372, CCDS91598

Canonical transcript exons

ENST00000534921 — 9 exons

Exon	Start	End
ENSE00000747489	114522879	114523091
ENSE00001265756	114552852	114552880
ENSE00002214915	114551103	114551211
ENSE00002299356	114551383	114551441
ENSE00002309562	114551974	114552085
ENSE00002310551	114559798	114559881
ENSE00003480116	114530175	114530908
ENSE00003667364	114527840	114527901
ENSE00003814551	114518934	114522503

Expression profiles

Bgee: expression breadth broad, 81 present calls, max score 97.31.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1851 / max 131.6316, expressed in 8 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
122371	0.1542	7
122370	0.0309	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
rectum	UBERON:0001052	97.31	gold quality
mucosa of sigmoid colon	UBERON:0004993	96.98	gold quality
colonic mucosa	UBERON:0000317	96.41	gold quality
mucosa of transverse colon	UBERON:0004991	94.34	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.35	gold quality
transverse colon	UBERON:0001157	87.88	gold quality
colonic epithelium	UBERON:0000397	85.68	gold quality
large intestine	UBERON:0000059	76.90	gold quality
calcaneal tendon	UBERON:0003701	76.46	gold quality
colon	UBERON:0001155	76.11	gold quality
caecum	UBERON:0001153	75.08	gold quality
intestine	UBERON:0000160	74.43	gold quality
vermiform appendix	UBERON:0001154	74.42	gold quality
small intestine Peyer’s patch	UBERON:0003454	70.36	gold quality
sperm	CL:0000019	69.13	gold quality
small intestine	UBERON:0002108	67.96	gold quality
left testis	UBERON:0004533	64.81	gold quality
tendon	UBERON:0000043	64.63	gold quality
jejunal mucosa	UBERON:0000399	63.00	gold quality
testis	UBERON:0000473	62.85	gold quality
epithelium of nasopharynx	UBERON:0001951	61.77	gold quality
right testis	UBERON:0004534	60.78	gold quality
upper leg skin	UBERON:0004262	60.35	gold quality
smooth muscle tissue	UBERON:0001135	60.17	gold quality
duodenum	UBERON:0002114	59.53	gold quality
heart right ventricle	UBERON:0002080	57.81	gold quality
buccal mucosa cell	CL:0002336	57.57	gold quality
amniotic fluid	UBERON:0000173	57.27	gold quality
vena cava	UBERON:0004087	55.78	gold quality
jejunum	UBERON:0002115	55.34	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	50.11
E-ANND-3	yes	5.59

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting NXPE1, 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-4673	100.00	66.64	1490
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-8062	99.88	68.43	995
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-3678-3P	99.31	67.10	1432
HSA-MIR-1911-3P	99.15	66.17	528
HSA-MIR-10B-3P	99.04	66.98	988
HSA-MIR-218-1-3P	98.63	67.97	832
HSA-MIR-5089-5P	98.45	66.06	1388
HSA-MIR-4654	95.86	65.72	751
HSA-MIR-324-5P	95.68	65.20	560
HSA-MIR-217-3P	95.67	68.42	1000
HSA-MIR-4769-5P	95.37	66.09	570
HSA-MIR-7975	95.04	66.76	516
HSA-MIR-3622B-5P	94.62	64.58	835

Cross-species orthologs

0 orthologs

Paralogs (3): NXPE4 (ENSG00000137634), NXPE3 (ENSG00000144815), NXPE2 (ENSG00000204361)

Protein

Protein identifiers

NXPE family member 1 — Q8N323 (reviewed: Q8N323)

Alternative names: Protein FAM55A

All UniProt accessions (3): Q8N323, F5H0Y6, F5H6W7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the NXPE family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N323-1	1	yes
Q8N323-2	2

RefSeq proteins (3): NP_001354882, NP_001382433, NP_689528 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013783	Ig-like_fold	Homologous_superfamily
IPR014756	Ig_E-set	Homologous_superfamily
IPR026845	NXPH/NXPE	Family
IPR057106	NXPE4_C	Domain

Pfam: PF06312, PF24536

UniProt features (8 total): glycosylation site 2, sequence variant 2, signal peptide 1, chain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
9PJA	ELECTRON MICROSCOPY	2.8

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N323-F1	91.49	0.83

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (2): 39, 211

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 23 (showing top): GSE13887_HEALTHY_VS_LUPUS_RESTING_CD4_TCELL_UP, ALX4_TARGET_GENES, DLX2_TARGET_GENES, MSX1_TARGET_GENES, MIR5582_3P, MIR4654, MIR4769_5P, MIR1911_3P, HBZ_TARGET_GENES, GSE7459_UNTREATED_VS_IL6_TREATED_ACT_CD4_TCELL_DN, GSE29617_CTRL_VS_DAY7_TIV_FLU_VACCINE_PBMC_2008_UP, GSE3565_DUSP1_VS_WT_SPLENOCYTES_POST_LPS_INJECTION_UP, GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_6H_UP, GSE6259_FLT3L_INDUCED_VS_WT_SPLENIC_DC_33D1_POS_DN, GSE21360_SECONDARY_VS_TERTIARY_MEMORY_CD8_TCELL_DN

GO Biological Process (0):

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

GO Cellular Component (2): extracellular region (GO:0005576), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
binding	1

Protein interactions and networks

STRING

228 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NXPE1	ARHGAP9	Q9BRR9	531
NXPE1	TENM2	Q9NT68	501
NXPE1	KIF5A	Q12840	478
NXPE1	ZNF385C	Q66K41	446
NXPE1	C11orf71	Q6IPW1	434
NXPE1	MDM2	Q00987	387
NXPE1	REXO2	Q9Y3B8	380
NXPE1	OVCA2	Q8WZ82	360
NXPE1	SLC60A1	Q8N468	359
NXPE1	PCED1B	Q96HM7	353
NXPE1	POU2AF3	A8K830	348
NXPE1	TIMM10B	Q9Y5J6	322
NXPE1	CSGALNACT2	Q8N6G5	316
NXPE1	EXD2	Q9NVH0	313
NXPE1	SPINK4	O60575	312

IntAct

16 interactions, top by confidence:

A	B	Type	Score
CALR	NXPE1	psi-mi:“MI:0915”(physical association)	0.560
NXPE1	CDH1	psi-mi:“MI:0915”(physical association)	0.560
DLST	NXPE1	psi-mi:“MI:0915”(physical association)	0.560
NXPE1	AHCYL1	psi-mi:“MI:0915”(physical association)	0.560
NXPE1	NEK7	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (3): VARS (Cross-Linking-MS (XL-MS)), NXPE1 (Co-fractionation), NXPE1 (Co-fractionation)

ESM2 similar proteins: A2VDP6, A4D0V7, B1WB06, F1N2K1, O43548, P06802, P15396, P22413, P50127, P79949, P97259, Q05004, Q08834, Q08BN9, Q09328, Q14C87, Q14DG7, Q2TU62, Q3L7M0, Q3U095, Q52KP5, Q5R748, Q5RCA5, Q5XI89, Q5ZLK4, Q6AX23, Q6DNG6, Q6UWF7, Q6ZXA0, Q76HP2, Q76HP3, Q86UX2, Q8BG22, Q8C7K6, Q8K1B9, Q8N323, Q8NCG5, Q8NHY0, Q8R4G6, Q8VI38

Diamond homologs: A2VDP6, Q05004, Q08BN9, Q3U095, Q52KP5, Q5RCA5, Q5XI89, Q6UWF7, Q8N323, Q969Y0, Q96DL1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	64
Likely benign	5
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1194 predictions. Top by Δscore:

Variant	Effect	Δscore
11:114522504:C:CC	acceptor_gain	0.9900
11:114522507:A:C	acceptor_gain	0.9900
11:114522501:GTG:G	acceptor_gain	0.9800
11:114530354:A:T	acceptor_gain	0.9800
11:114530869:A:T	acceptor_gain	0.9800
11:114522502:TG:T	acceptor_gain	0.9700
11:114522503:GCTG:G	acceptor_loss	0.9700
11:114522504:C:CA	acceptor_loss	0.9700
11:114522505:T:A	acceptor_loss	0.9700
11:114527838:A:AC	donor_gain	0.9700
11:114527839:C:CC	donor_gain	0.9700
11:114522507:A:AC	acceptor_gain	0.9600
11:114552881:C:CC	acceptor_gain	0.9600
11:114522499:CAGTG:C	acceptor_gain	0.9500
11:114551144:C:CT	donor_gain	0.9500
11:114551145:T:TT	donor_gain	0.9500
11:114559794:TCAC:T	donor_loss	0.9500
11:114559795:CACC:C	donor_loss	0.9500
11:114559796:ACC:A	donor_loss	0.9500
11:114559797:C:A	donor_loss	0.9500
11:114522499:CAG:C	acceptor_gain	0.9200
11:114530347:C:CT	acceptor_gain	0.9200
11:114523092:C:G	acceptor_gain	0.9100
11:114559796:A:AC	donor_gain	0.9100
11:114559797:C:CC	donor_gain	0.9100
11:114522516:C:CT	acceptor_loss	0.9000
11:114523091:TCTG:T	acceptor_gain	0.9000
11:114559797:CCT:C	donor_gain	0.9000
11:114552879:CA:C	acceptor_gain	0.8900
11:114543659:C:A	donor_gain	0.8800

AlphaMissense

3644 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:114530381:A:C	F209L	0.983
11:114530381:A:T	F209L	0.983
11:114530383:A:G	F209L	0.983
11:114530705:G:C	S101R	0.972
11:114530705:G:T	S101R	0.972
11:114530707:T:G	S101R	0.972
11:114522909:A:G	W360R	0.969
11:114522909:A:T	W360R	0.969
11:114530349:C:G	C220S	0.967
11:114530350:A:T	C220S	0.967
11:114522184:C:A	K476N	0.966
11:114522184:C:G	K476N	0.966
11:114530277:C:G	C244S	0.964
11:114530278:A:T	C244S	0.964
11:114522420:A:G	W398R	0.963
11:114522420:A:T	W398R	0.963
11:114530316:C:G	C231S	0.962
11:114530317:A:T	C231S	0.962
11:114530276:A:C	C244W	0.956
11:114530382:A:C	F209C	0.955
11:114530282:G:C	F242L	0.949
11:114530282:G:T	F242L	0.949
11:114530284:A:G	F242L	0.949
11:114530612:C:A	K132N	0.949
11:114530612:C:G	K132N	0.949
11:114530393:G:C	F205L	0.947
11:114530393:G:T	F205L	0.947
11:114530395:A:G	F205L	0.947
11:114530350:A:G	C220R	0.944
11:114530277:C:T	C244Y	0.943

dbSNP variants (sampled 300 via entrez): RS1000161844 (11:114559299 C>T), RS1000205093 (11:114553896 A>G), RS1000243684 (11:114536052 T>C), RS1000291564 (11:114547053 C>G), RS1000294197 (11:114540649 C>T), RS1000455453 (11:114540050 C>T), RS1000598727 (11:114529140 G>A), RS1000759373 (11:114520202 C>G,T), RS1000767187 (11:114560683 C>T), RS1000769769 (11:114523269 T>G), RS1000907190 (11:114548857 C>G), RS1000912236 (11:114536802 C>A), RS1000945642 (11:114541755 A>T), RS1000948281 (11:114560282 T>C), RS1000948383 (11:114529351 A>G)

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

4 associations (top):

Study	Trait	p-value
GCST001728_5	Ulcerative colitis	5.000000e-17
GCST004131_119	Inflammatory bowel disease	2.000000e-06
GCST004133_61	Ulcerative colitis	2.000000e-09
GCST005537_81	Chronic inflammatory diseases (ankylosing spondylitis, Crohn’s disease, psoriasis, primary sclerosing cholangitis, ulcerative colitis) (pleiotropy)	2.000000e-14

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Grape Seed Proanthocyanidins	decreases expression, affects cotreatment	1
Catechin	affects cotreatment, decreases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	decreases expression	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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