CTXND1

Summary

CTXND1 (cortexin domain containing 1, HGNC:50507) is a protein-coding gene on chromosome 15q25.1, encoding Cortexin domain-containing 1 protein (A0A1B0GTU2).

Predicted to be located in membrane.

Source: NCBI Gene 100996492 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001352888

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:50507
Approved symbol	CTXND1
Name	cortexin domain containing 1
Location	15q25.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000259417
Ensembl biotype	protein_coding
Entrez	100996492

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000560778, ENST00000851084, ENST00000851085, ENST00000851086, ENST00000851087, ENST00000941912

RefSeq mRNA: 1 — MANE Select: NM_001352888 NM_001352888

CCDS: CCDS86481

Canonical transcript exons

ENST00000560778 — 3 exons

Exon	Start	End
ENSE00002541602	80252007	80252213
ENSE00002551195	80203589	80203740
ENSE00002563845	80195481	80202014

Expression profiles

Bgee: expression breadth ubiquitous, 180 present calls, max score 88.51.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.7932 / max 66.1284, expressed in 171 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
151202	0.6511	147
151203	0.1421	84

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
CA1 field of hippocampus	UBERON:0003881	88.51	gold quality
pancreatic ductal cell	CL:0002079	84.34	silver quality
Ammon’s horn	UBERON:0001954	83.95	gold quality
amygdala	UBERON:0001876	83.43	gold quality
temporal lobe	UBERON:0001871	79.98	gold quality
frontal pole	UBERON:0002795	79.78	gold quality
medial globus pallidus	UBERON:0002477	79.08	gold quality
caudate nucleus	UBERON:0001873	78.57	gold quality
hypothalamus	UBERON:0001898	78.25	gold quality
nucleus accumbens	UBERON:0001882	78.04	gold quality
Brodmann (1909) area 10	UBERON:0013541	77.83	gold quality
middle frontal gyrus	UBERON:0002702	77.69	gold quality
putamen	UBERON:0001874	77.50	gold quality
paraflocculus	UBERON:0005351	77.46	gold quality
cingulate cortex	UBERON:0003027	77.10	gold quality
entorhinal cortex	UBERON:0002728	77.09	gold quality
anterior cingulate cortex	UBERON:0009835	77.03	gold quality
right lobe of liver	UBERON:0001114	76.45	gold quality
globus pallidus	UBERON:0001875	76.45	gold quality
endothelial cell	CL:0000115	75.74	silver quality
substantia nigra	UBERON:0002038	75.40	gold quality
liver	UBERON:0002107	75.33	gold quality
telencephalon	UBERON:0001893	75.11	gold quality
midbrain	UBERON:0001891	74.41	gold quality
cerebral cortex	UBERON:0000956	74.06	gold quality
prefrontal cortex	UBERON:0000451	73.92	gold quality
tibia	UBERON:0000979	73.57	gold quality
cerebellar vermis	UBERON:0004720	73.32	gold quality
forebrain	UBERON:0001890	72.92	gold quality
neocortex	UBERON:0001950	72.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.14

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ctxnd1	ENSMUSG00000097789
rattus_norvegicus	Ctxnd1	ENSRNOG00000084604

Protein

Protein identifiers

Cortexin domain-containing 1 protein — A0A1B0GTU2 (reviewed: A0A1B0GTU2)

All UniProt accessions (1): A0A1B0GTU2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001339817* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR020066	Cortexin	Family

Pfam: PF11057

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GTU2-F1	80.09	0.41

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 24 (showing top): JAEGER_METASTASIS_DN, XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN, CAIRO_HEPATOBLASTOMA_CLASSES_DN, SHEN_SMARCA2_TARGETS_DN, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP, HUTTMANN_B_CLL_POOR_SURVIVAL_UP, CBX7_TARGET_GENES, HAND1_TARGET_GENES, HSD17B8_TARGET_GENES, RYBP_TARGET_GENES, ZNF22_TARGET_GENES, DESCARTES_FETAL_EYE_ASTROCYTES, DESCARTES_FETAL_HEART_SCHWANN_CELLS, DESCARTES_FETAL_KIDNEY_URETERIC_BUD_CELLS, DESCARTES_FETAL_LIVER_HEPATOBLASTS

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

80 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CTXND1	AKNAD1	Q5T1N1	520
CTXND1	ASB5	Q8WWX0	437
CTXND1	CYYR1	Q96J86	419
CTXND1	ART5	Q96L15	413
CTXND1	AKR1B15	C9JRZ8	395
CTXND1	CPNE4	Q96A23	377
CTXND1	APOBR	Q0VD83	373
CTXND1	C1QTNF4	Q9BXJ3	371
CTXND1	DCLK2	Q8N568	366
CTXND1	ABCA10	Q8WWZ4	349
CTXND1	MED27	Q6P2C8	324
CTXND1	MBOAT2	Q6ZWT7	315
CTXND1	ZNF263	O14978	310
CTXND1	CHI3L2	Q15782	297
CTXND1	CMIP	Q8IY22	297

IntAct

0 interactions, top by confidence:

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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

388 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:80201794:C:A	W52C	0.998
15:80201794:C:G	W52C	0.998
15:80201844:A:G	C36R	0.996
15:80201874:A:G	C26R	0.995
15:80201796:A:G	W52R	0.994
15:80201796:A:T	W52R	0.994
15:80201822:G:A	P43L	0.993
15:80201822:G:T	P43H	0.992
15:80201823:G:A	P43S	0.992
15:80201825:T:C	D42G	0.990
15:80201840:G:T	A37D	0.990
15:80201842:A:C	C36W	0.988
15:80201843:C:T	C36Y	0.988
15:80201841:C:G	A37P	0.987
15:80201889:A:G	C21R	0.987
15:80201810:A:G	I47T	0.986
15:80201846:C:G	R35P	0.986
15:80201823:G:T	P43T	0.985
15:80201864:A:T	L29H	0.985
15:80201864:A:C	L29R	0.984
15:80201864:A:G	L29P	0.984
15:80201823:G:C	P43A	0.983
15:80201831:A:T	I40N	0.983
15:80201820:A:C	Y44D	0.982
15:80201819:T:C	Y44C	0.979
15:80201820:A:G	Y44H	0.979
15:80201822:G:C	P43R	0.979
15:80201825:T:A	D42V	0.979
15:80201825:T:G	D42A	0.974
15:80201876:A:C	L25R	0.974

dbSNP variants (sampled 300 via entrez): RS1000044669 (15:80239464 G>A), RS1000073896 (15:80235895 T>C,G), RS1000088319 (15:80241234 G>A,T), RS1000140483 (15:80252669 T>G), RS1000172079 (15:80250787 T>C), RS1000241094 (15:80218022 T>C), RS1000283646 (15:80216276 C>G), RS1000314332 (15:80217627 A>G), RS1000356874 (15:80216128 A>G), RS1000377636 (15:80244296 G>A), RS1000496355 (15:80252350 G>T), RS1000650346 (15:80219321 G>A), RS1000688270 (15:80214460 A>C,G), RS1000719653 (15:80225414 A>G), RS1000747275 (15:80253874 A>C,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): megacolon (MONDO:0001273)

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST009996_7	HDL cholesterol levels	8.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007805	HDL cholesterol change measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D008531	Megacolon	C06.405.469.158.701

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
Tobacco Smoke Pollution	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04340856	Not specified	COMPLETED	Retrospective, Uncontrolled Cohort Study on the Therapy of Chronic Megalon
NCT07470892	Not specified	NOT_YET_RECRUITING	Preoperative Fish Oil PN and Prognosis After Constipation Surgery