CTXN3

Summary

CTXN3 (cortexin 3, HGNC:31110) is a protein-coding gene on chromosome 5q23.2, encoding Cortexin-3 (Q4LDR2).

Predicted to be located in membrane.

Source: NCBI Gene 613212 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 10 total
• MANE Select transcript: NM_001048252

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31110
Approved symbol	CTXN3
Name	cortexin 3
Location	5q23.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000205279
Ensembl biotype	protein_coding
OMIM	618746
Entrez	613212

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000379445, ENST00000395322, ENST00000514851, ENST00000620385

RefSeq mRNA: 2 — MANE Select: NM_001048252 NM_001048252, NM_001127385

CCDS: CCDS34221

Canonical transcript exons

ENST00000379445 — 3 exons

Exon	Start	End
ENSE00001481062	127657423	127658630
ENSE00001481063	127653317	127653423
ENSE00001481064	127649082	127649388

Expression profiles

Bgee: expression breadth broad, 95 present calls, max score 95.38.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.8715 / max 112.8030, expressed in 108 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
58343	0.3542	75
58342	0.2735	76
58345	0.1236	60
58344	0.0987	46
58346	0.0214	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	95.38	gold quality
pons	UBERON:0000988	91.02	gold quality
Brodmann (1909) area 23	UBERON:0013554	88.73	gold quality
endothelial cell	CL:0000115	87.92	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	84.15	gold quality
Brodmann (1909) area 9	UBERON:0013540	83.78	gold quality
adult mammalian kidney	UBERON:0000082	83.54	gold quality
right frontal lobe	UBERON:0002810	83.06	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.82	gold quality
substantia nigra pars compacta	UBERON:0001965	81.87	gold quality
prefrontal cortex	UBERON:0000451	81.33	gold quality
frontal cortex	UBERON:0001870	80.42	gold quality
anterior cingulate cortex	UBERON:0009835	79.58	gold quality
middle temporal gyrus	UBERON:0002771	79.22	gold quality
neocortex	UBERON:0001950	78.81	gold quality
substantia nigra	UBERON:0002038	77.93	gold quality
vastus lateralis	UBERON:0001379	77.39	silver quality
substantia nigra pars reticulata	UBERON:0001966	77.22	gold quality
midbrain	UBERON:0001891	76.92	gold quality
cerebral cortex	UBERON:0000956	76.22	gold quality
superior frontal gyrus	UBERON:0002661	75.42	gold quality
quadriceps femoris	UBERON:0001377	75.30	silver quality
kidney	UBERON:0002113	75.29	gold quality
adult organism	UBERON:0007023	75.16	gold quality
lateral nuclear group of thalamus	UBERON:0002736	74.84	gold quality
hypothalamus	UBERON:0001898	72.85	gold quality
renal medulla	UBERON:0000362	72.24	gold quality
tibialis anterior	UBERON:0001385	71.18	silver quality
Brodmann (1909) area 46	UBERON:0006483	70.74	gold quality
pituitary gland	UBERON:0000007	70.36	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-56	yes	361.00
E-ANND-3	no	2.61

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

42 targeting CTXN3, 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-4803	99.98	71.99	3117
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-5002-5P	99.76	70.84	1763
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-6505-5P	99.73	69.25	1595
HSA-MIR-4465	99.71	72.56	2096
HSA-MIR-29B-2-5P	99.67	68.98	1726
HSA-MIR-6758-3P	99.57	67.55	1078
HSA-MIR-5004-3P	99.54	68.27	1371
HSA-MIR-5007-3P	99.51	68.14	1242
HSA-MIR-4643	99.49	67.63	1791
HSA-MIR-217-5P	99.49	69.93	1419
HSA-MIR-183-3P	99.41	69.41	1598
HSA-MIR-377-3P	99.37	70.18	1905
HSA-MIR-4641	99.28	66.64	744
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-6807-3P	99.15	69.23	1275
HSA-MIR-4705	99.10	69.10	1091
HSA-MIR-1288-5P	98.85	67.01	734
HSA-MIR-887-5P	98.82	65.90	1347
HSA-MIR-1246	98.54	66.21	959

Literature-anchored findings (GeneRIF, showing 3)

• Selective expression of CTXN3 in the kidney and brain, the amino acid identity to cortexin, and its high conservation among different species indicate that CTXN3 may be involved in a process specifically restricted to kidney and brain tissue function. (PMID:17786280)
• Two single nucleotide polymophisms of the CTXN3 and SLC12A2 genes are associated with risk of schizophrenia in a Thai population. (PMID:22643131)
• altered expression of cortexin 3, either alone, or in parallel with changes in disrupted-in-schizophrenia 1, could subtly perturb GABAergic neurotransmission (PMID:25889058)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ctxn3	ENSDARG00000114472
mus_musculus	Ctxn3	ENSMUSG00000069372
rattus_norvegicus	Ctxn3	ENSRNOG00000022957

Paralogs (2): CTXN1 (ENSG00000178531), CTXN2 (ENSG00000233932)

Protein

Protein identifiers

Cortexin-3 — Q4LDR2 (reviewed: Q4LDR2)

Alternative names: Kidney and brain-expressed protein

All UniProt accessions (1): Q4LDR2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the cortexin family.

RefSeq proteins (2): NP_001041717, NP_001120857 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR020066	Cortexin	Family

Pfam: PF11057

UniProt features (4 total): sequence variant 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q4LDR2-F1	71.02	0.21

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 30 (showing top): GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_DN, GSE13522_WT_VS_IFNG_KO_SKIN_DN, MARTENS_TRETINOIN_RESPONSE_UP, MIR1297, MIR26A_5P, MIR26B_5P, MIR4465, MIR5010_3P, MIR5003_3P, MIR5002_5P, MIR4279, MIR6505_5P, MIR4643, MIR6758_3P, MIR4641

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

906 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CTXN3	WWC1	Q8IX03	764
CTXN3	NF2	P35240	670
CTXN3	SLC12A2	P55011	578
CTXN3	DDN	O94850	549
CTXN3	RSRC1	Q96IZ7	449
CTXN3	TEKT3	Q9BXF9	441
CTXN3	APP	P05067	440
CTXN3	RSPH9	Q9H1X1	423
CTXN3	MINAR2	P59773	417
CTXN3	CCDC192	P0DO97	397
CTXN3	KRTAP8-1	Q8IUC2	389
CTXN3	GFER	P55789	384
CTXN3	COL5A2	P05997	381
CTXN3	ONECUT2	O95948	381
CTXN3	KIF25	Q9UIL4	375

IntAct

180 interactions, top by confidence:

A	B	Type	Score
CTXN3	IFNLR1	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	CLRN1	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	PLPP5	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	CERS4	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	LAPTM4B	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	AQP9	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	LHFPL5	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	CD300E	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	LDLRAD1	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	EDA	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	CLEC7A	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	KASH5	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	MGST2	psi-mi:“MI:0915”(physical association)	0.560
FUT7	CTXN3	psi-mi:“MI:0915”(physical association)	0.560
BIK	CTXN3	psi-mi:“MI:0915”(physical association)	0.560
KLRC1	CTXN3	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	GPR61	psi-mi:“MI:0915”(physical association)	0.560
OPRM1	CTXN3	psi-mi:“MI:0915”(physical association)	0.560
STOM	CTXN3	psi-mi:“MI:0915”(physical association)	0.560
ATP1B3	CTXN3	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	CREB3L1	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	PACC1	psi-mi:“MI:0915”(physical association)	0.560
TMPRSS2	CTXN3	psi-mi:“MI:0915”(physical association)	0.560
OPRD1	CTXN3	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	TMEM106C	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (60): CTXN3 (Two-hybrid), CTXN3 (Two-hybrid), CTXN3 (Two-hybrid), CTXN3 (Two-hybrid), CTXN3 (Two-hybrid), CTXN3 (Two-hybrid), CTXN3 (Two-hybrid), CTXN3 (Two-hybrid), CTXN3 (Two-hybrid), CTXN3 (Two-hybrid), CTXN3 (Two-hybrid), CTXN3 (Two-hybrid), CTXN3 (Two-hybrid), CTXN3 (Two-hybrid), CTXN3 (Two-hybrid)

ESM2 similar proteins: A0A1B0GST9, A0A1B0GTU2, A0A1B0GV90, A0A590UK83, A2RRL7, A7S641, A8WG88, A9JTJ0, B9X187, K7EJ46, O00168, O08589, O13001, P0C2S0, P15383, P41237, P56513, P60606, P63160, P63161, Q04645, Q04646, Q04679, Q04680, Q0P467, Q28EH9, Q3SZX0, Q3UJ81, Q3URE8, Q3ZBP2, Q4LDR2, Q4R6L9, Q502I1, Q592E4, Q5XF36, Q6AXF6, Q6NWH5, Q6PBK8, Q6Q3F5, Q71RC9

Diamond homologs: A0A1B0GQX3, A0A1B0GST9, A0A1B0GTU2, A0A1B0GV90, P0C2S0, P41237, P60606, Q3URE8, Q4LDR2, Q8K129, Q592E4, Q8BXZ0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	10
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

477 predictions. Top by Δscore:

Variant	Effect	Δscore
5:127652188:GATCT:G	donor_gain	1.0000
5:127652198:TTTTA:T	donor_gain	1.0000
5:127653315:A:AG	acceptor_gain	0.9900
5:127653316:G:GA	acceptor_gain	0.9900
5:127653316:GT:G	acceptor_gain	0.9900
5:127653316:GTATT:G	acceptor_gain	0.9900
5:127653420:GGCT:G	donor_gain	0.9900
5:127653421:GCT:G	donor_gain	0.9900
5:127653421:GCTG:G	donor_gain	0.9900
5:127653424:G:GG	donor_gain	0.9900
5:127657421:A:AG	acceptor_gain	0.9900
5:127657422:G:GA	acceptor_gain	0.9900
5:127652189:A:G	donor_gain	0.9800
5:127653397:A:T	donor_gain	0.9800
5:127653419:TGGCT:T	donor_gain	0.9800
5:127653420:GGCTG:G	donor_gain	0.9800
5:127657420:CAG:C	acceptor_loss	0.9800
5:127657421:A:C	acceptor_loss	0.9800
5:127657422:GAT:G	acceptor_gain	0.9800
5:127657422:GATA:G	acceptor_gain	0.9800
5:127649385:CCAGG:C	donor_loss	0.9700
5:127649386:CAG:C	donor_loss	0.9700
5:127649387:AG:A	donor_loss	0.9700
5:127649388:GGTA:G	donor_loss	0.9700
5:127649389:G:T	donor_loss	0.9700
5:127649390:T:A	donor_loss	0.9700
5:127652818:G:GT	donor_gain	0.9700
5:127657422:GA:G	acceptor_gain	0.9700
5:127657422:GATAA:G	acceptor_gain	0.9700
5:127649208:G:T	donor_gain	0.9600

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000031083 (5:127657959 A>T), RS1000956116 (5:127650644 T>C), RS1001042831 (5:127653108 G>A), RS1001096554 (5:127652853 T>A), RS1001259014 (5:127658929 C>T), RS1001339821 (5:127648250 A>G), RS1001644384 (5:127648355 G>C), RS1001650279 (5:127653881 T>C), RS1001676900 (5:127648541 C>G,T), RS1001889406 (5:127654755 C>T), RS1001992885 (5:127649846 C>T), RS1002099095 (5:127654137 T>C,G), RS1002649616 (5:127652581 G>A,C), RS1002758118 (5:127647597 C>A), RS1003051328 (5:127655958 A>G)

Disease associations

OMIM: gene MIM:618746 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST000271_1	Brain imaging in schizophrenia (dorsolateral prefrontal cortex interaction)	9.000000e-08
GCST002359_1	Plasma amyloid beta peptide concentrations (ABx-42)	2.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005660	plasma beta-amyloid 1-42 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
entinostat	increases expression	1
bisphenol S	decreases methylation	1
Vorinostat	increases expression	1
Ethanol	decreases expression, affects cotreatment	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Folic Acid	affects cotreatment, decreases expression	1
Rotenone	decreases expression	1
Thimerosal	increases expression	1
Valproic Acid	decreases methylation	1
1-Methyl-4-phenylpyridinium	decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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