PCNX4

Summary

PCNX4 (pecanex 4, HGNC:20349) is a protein-coding gene on chromosome 14q23.1, encoding Pecanex-like protein 4 (Q63HM2).

Predicted to be located in membrane.

Source: NCBI Gene 64430 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_001330177

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20349
Approved symbol	PCNX4
Name	pecanex 4
Location	14q23.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000126773
Ensembl biotype	protein_coding
Entrez	64430

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 8 protein_coding, 3 retained_intron, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000317623, ENST00000391611, ENST00000406854, ENST00000406949, ENST00000483571, ENST00000553513, ENST00000553898, ENST00000554534, ENST00000555569, ENST00000555740, ENST00000555929, ENST00000556360, ENST00000556907, ENST00000868337, ENST00000868338, ENST00000913742

RefSeq mRNA: 2 — MANE Select: NM_001330177 NM_001330177, NM_022495

CCDS: CCDS32091, CCDS81809

Canonical transcript exons

ENST00000406854 — 11 exons

Exon	Start	End
ENSE00001509391	60107586	60108327
ENSE00001652612	60118329	60118692
ENSE00001731244	60114974	60115461
ENSE00003478017	60114700	60114879
ENSE00003534032	60121196	60121299
ENSE00003583042	60115941	60116060
ENSE00003607083	60125637	60125823
ENSE00003664772	60133970	60148221
ENSE00003690635	60124218	60125251
ENSE00003692727	60115719	60115819
ENSE00003842313	60091923	60092419

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 98.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 31.2789 / max 185.0766, expressed in 1813 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
139855	21.5131	1801
139857	5.4584	1677
139860	2.1320	1148
139858	1.0588	753
139856	0.5607	322
139859	0.3878	186
139861	0.1680	45

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	98.77	gold quality
ganglionic eminence	UBERON:0004023	97.58	gold quality
cortical plate	UBERON:0005343	96.97	gold quality
adrenal tissue	UBERON:0018303	96.17	gold quality
stromal cell of endometrium	CL:0002255	96.09	gold quality
right uterine tube	UBERON:0001302	95.85	gold quality
tendon of biceps brachii	UBERON:0008188	95.35	gold quality
adenohypophysis	UBERON:0002196	94.48	gold quality
left ovary	UBERON:0002119	94.45	gold quality
right ovary	UBERON:0002118	94.42	gold quality
pituitary gland	UBERON:0000007	93.83	gold quality
ovary	UBERON:0000992	93.71	gold quality
bronchial epithelial cell	CL:0002328	93.64	gold quality
secondary oocyte	CL:0000655	93.16	gold quality
mucosa of paranasal sinus	UBERON:0005030	93.13	gold quality
oocyte	CL:0000023	93.09	gold quality
tendon	UBERON:0000043	92.38	gold quality
choroid plexus epithelium	UBERON:0003911	92.25	gold quality
right adrenal gland cortex	UBERON:0035827	92.10	gold quality
right adrenal gland	UBERON:0001233	91.71	gold quality
body of uterus	UBERON:0009853	91.71	gold quality
colonic epithelium	UBERON:0000397	91.70	gold quality
left adrenal gland	UBERON:0001234	91.66	gold quality
calcaneal tendon	UBERON:0003701	91.63	gold quality
endocervix	UBERON:0000458	91.60	gold quality
metanephros cortex	UBERON:0010533	91.56	gold quality
left adrenal gland cortex	UBERON:0035825	91.41	gold quality
tibia	UBERON:0000979	91.38	gold quality
germinal epithelium of ovary	UBERON:0001304	91.35	gold quality
endometrium	UBERON:0001295	91.34	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	35.12
E-GEOD-137537	no	642.93
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting PCNX4, 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-4533	100.00	69.48	2758
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-323A-3P	99.79	70.30	1739
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948
HSA-MIR-8084	99.73	69.57	1760
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-651-5P	99.64	68.49	1104
HSA-MIR-6752-5P	99.59	67.32	1243
HSA-MIR-3942-3P	99.57	69.03	2854
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-582-5P	99.47	70.79	2635
HSA-MIR-6507-3P	99.35	67.32	1059

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	pcnx4	ENSDARG00000060785
mus_musculus	Pcnx4	ENSMUSG00000034501
rattus_norvegicus	AABR07064804.1	ENSRNOG00000005568

Paralogs (3): PCNX1 (ENSG00000100731), PCNX2 (ENSG00000135749), PCNX3 (ENSG00000197136)

Protein

Protein identifiers

Pecanex-like protein 4 — Q63HM2 (reviewed: Q63HM2)

Alternative names: Hepatitis C virus F protein-binding protein 2, Pecanex homolog protein 4

All UniProt accessions (8): Q63HM2, B5MC47, B6ZDM2, H0YIY3, H0YJ84, H0YJN3, H0YJV9, H9KV87

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the pecanex family.

RefSeq proteins (2): NP_001317106, NP_071940 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007735	Pecanex_C	Domain
IPR039797	Pecanex	Family

Pfam: PF05041

UniProt features (23 total): transmembrane region 15, sequence variant 3, glycosylation site 2, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q63HM2-F1	78.42	0.40

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): 1120, 1147

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 79 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, BEIER_GLIOMA_STEM_CELL_DN, chr14q23, POU3F2_02, WGGAATGY_TEF1_Q6, KIM_WT1_TARGETS_DN, JOHNSTONE_PARVB_TARGETS_3_DN, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, DELACROIX_RARG_BOUND_MEF, ARNT2_TARGET_GENES, ATF5_TARGET_GENES, FEV_TARGET_GENES, GLI3_TARGET_GENES, GUCY1B1_TARGET_GENES, HES4_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

372 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PCNX4	CEP44	Q9C0F1	445
PCNX4	MIDEAS	Q6PJG2	397
PCNX4	RPRD2	Q5VT52	395
PCNX4	DHRS7	Q9Y394	374
PCNX4	SLC35A4	Q96G79	374
PCNX4	TBC1D9	Q6ZT07	368
PCNX4	UNC79	Q9P2D8	366
PCNX4	RPS12	P25398	339
PCNX4	RALGAPA1	Q6GYQ0	337
PCNX4	FAXDC2	Q96IV6	336
PCNX4	CCDC141	Q6ZP82	325
PCNX4	MDGA2	Q7Z553	323
PCNX4	PILRB	Q9UKJ0	320
PCNX4	CCNI	Q14094	317
PCNX4	BCAS2	O75934	305

IntAct

11 interactions, top by confidence:

A	B	Type	Score
PCNX4		psi-mi:“MI:0915”(physical association)	0.510
	PCNX4	psi-mi:“MI:0915”(physical association)	0.510
FBP1	PCNX4	psi-mi:“MI:0915”(physical association)	0.370
PCNX4	DISC1	psi-mi:“MI:0915”(physical association)	0.000
PCNX4	CEP63	psi-mi:“MI:0915”(physical association)	0.000
PCNX4	MTNR1B	psi-mi:“MI:0915”(physical association)	0.000
DISC1	PCNX4	psi-mi:“MI:0915”(physical association)	0.000
CEP63	PCNX4	psi-mi:“MI:0915”(physical association)	0.000
PCNX4	wecE	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (10): PCNXL4 (Two-hybrid), PCNXL4 (Two-hybrid), PCNXL4 (Affinity Capture-RNA), PCNXL4 (Affinity Capture-RNA), PCNXL4 (Affinity Capture-MS), PCNXL4 (Affinity Capture-RNA), PCNXL4 (Affinity Capture-MS), PCNXL4 (Affinity Capture-RNA), PCNXL4 (Two-hybrid), PCNXL4 (Two-hybrid)

ESM2 similar proteins: A0A291NUG3, A0A291NUI4, A0A291NUI5, A2AN08, A2CBW9, A2RUW7, A8E5V9, A9CB91, B8XX90, E1C7U0, E7F4N7, F1M391, O36397, P03207, P03246, P03247, P06501, P0C722, P0C723, P0CZ24, P11823, P11824, P18801, P37588, P49408, P52132, P68966, P68967, P77206, Q02189, Q10115, Q148F6, Q2HRD2, Q2KI99, Q3KPU7, Q3TBT3, Q3UVY5, Q5HZQ9, Q5K6N0, Q5XIF1

Diamond homologs: A2RUW7, A6NKB5, E9PSU6, P18490, Q3UVY5, Q5DU28, Q5HZQ9, Q63HM2, Q8VI59, Q96RV3, Q98UF7, Q9H6A9, Q9QYC1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2475 predictions. Top by Δscore:

Variant	Effect	Δscore
14:60115077:C:G	donor_gain	1.0000
14:60115089:T:G	donor_gain	1.0000
14:60115096:A:AG	donor_gain	1.0000
14:60115163:G:GT	donor_gain	1.0000
14:60115168:A:T	donor_gain	1.0000
14:60115936:T:A	acceptor_gain	1.0000
14:60115939:A:AC	acceptor_loss	1.0000
14:60115940:GGT:G	acceptor_gain	1.0000
14:60115940:GGTA:G	acceptor_gain	1.0000
14:60115940:GGTAT:G	acceptor_gain	1.0000
14:60116056:TACTG:T	donor_gain	1.0000
14:60116057:ACTG:A	donor_gain	1.0000
14:60116058:CTG:C	donor_gain	1.0000
14:60116059:TG:T	donor_gain	1.0000
14:60116059:TGG:T	donor_loss	1.0000
14:60116060:GG:G	donor_gain	1.0000
14:60116061:G:GA	donor_loss	1.0000
14:60116061:G:GG	donor_gain	1.0000
14:60116062:T:G	donor_loss	1.0000
14:60116850:G:GG	donor_gain	1.0000
14:60116888:A:G	donor_gain	1.0000
14:60118327:AGGTT:A	acceptor_gain	1.0000
14:60118328:GGTTG:G	acceptor_gain	1.0000
14:60121185:A:G	acceptor_gain	1.0000
14:60121191:TGTA:T	acceptor_loss	1.0000
14:60121193:TAGGT:T	acceptor_loss	1.0000
14:60121194:AGGTC:A	acceptor_loss	1.0000
14:60121195:G:A	acceptor_loss	1.0000
14:60121295:TTAAG:T	donor_loss	1.0000
14:60121296:TAAG:T	donor_loss	1.0000

AlphaMissense

7652 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:60134111:A:C	S1137R	0.996
14:60134113:T:A	S1137R	0.996
14:60134113:T:G	S1137R	0.996
14:60107674:G:C	K12N	0.995
14:60107674:G:T	K12N	0.995
14:60121241:G:C	R663P	0.995
14:60121249:T:A	W666R	0.994
14:60121249:T:C	W666R	0.994
14:60125761:T:A	W1069R	0.994
14:60125761:T:C	W1069R	0.994
14:60134143:T:A	N1147K	0.992
14:60134143:T:G	N1147K	0.992
14:60134145:T:C	L1148P	0.992
14:60134054:T:A	W1118R	0.991
14:60134054:T:C	W1118R	0.991
14:60124218:G:A	G683R	0.990
14:60124218:G:C	G683R	0.990
14:60134057:G:C	A1119P	0.990
14:60124257:G:C	A696P	0.989
14:60133992:T:C	L1097P	0.989
14:60134064:T:C	L1121P	0.989
14:60134092:C:A	N1130K	0.989
14:60134092:C:G	N1130K	0.989
14:60124218:G:T	G683W	0.988
14:60124917:T:A	W916R	0.988
14:60124917:T:C	W916R	0.988
14:60134106:G:C	R1135P	0.988
14:60107694:G:C	R19P	0.987
14:60121229:G:C	R659P	0.987
14:60124377:T:G	Y736D	0.987

dbSNP variants (sampled 300 via entrez): RS1000007676 (14:60129351 T>A,C), RS1000054383 (14:60145203 C>A,T), RS1000061515 (14:60110469 A>C), RS1000158104 (14:60104111 G>A,C,T), RS1000163854 (14:60144150 GAAT>G), RS1000227231 (14:60102829 A>T), RS1000262722 (14:60104768 C>G), RS1000353031 (14:60138818 G>A), RS1000354187 (14:60092850 C>G,T), RS1000376449 (14:60099064 G>GAGGAA), RS1000431412 (14:60138284 G>A,C), RS1000442058 (14:60098896 C>T), RS1000505381 (14:60145757 C>T), RS1000522860 (14:60121121 G>A,T), RS1000633170 (14:60105878 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

1 associations (top):

Study	Trait	p-value
GCST90000025_534	Appendicular lean mass	4.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	affects expression, decreases expression	3
Valproic Acid	affects expression, decreases expression	2
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
trichostatin A	affects expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
beta-lapachone	decreases expression, increases expression	1
K 7174	increases expression	1
Bortezomib	increases expression	1
Air Pollutants	increases abundance, decreases expression	1
Air Pollutants, Occupational	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Coal	decreases expression, increases abundance	1
Copper	affects binding, increases expression	1
Disulfiram	affects binding, increases expression	1
Doxorubicin	decreases expression	1
Nickel	decreases expression	1
Paraoxon	increases expression	1
Quercetin	decreases expression	1
Smoke	increases abundance, decreases expression	1
Vanadates	increases expression	1
Cyclosporine	decreases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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