CTXND2

Summary

CTXND2 (cortexin domain containing 2, HGNC:53440) is a protein-coding gene on chromosome 1q21.3, encoding Cortexin domain containing 2 (A0A1B0GV90).

Predicted to be located in membrane.

Source: NCBI Gene 100996521 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001384189

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53440
Approved symbol	CTXND2
Name	cortexin domain containing 2
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000283324
Ensembl biotype	protein_coding
Entrez	100996521

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000636087

RefSeq mRNA: 1 — MANE Select: NM_001384189 NM_001384189

CCDS: CCDS91049

Canonical transcript exons

ENST00000636087 — 2 exons

Exon	Start	End
ENSE00003791748	150887136	150887313
ENSE00003793610	150912242	150913292

Expression profiles

Bgee: expression breadth broad, 11 present calls, max score 82.72.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.72	gold quality
right uterine tube	UBERON:0001302	55.51	gold quality
placenta	UBERON:0001987	49.28	gold quality
fallopian tube	UBERON:0003889	43.29	gold quality
colonic epithelium	UBERON:0000397	41.46	gold quality
stromal cell of endometrium	CL:0002255	39.73	gold quality
skeletal muscle tissue	UBERON:0001134	37.27	silver quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
apex of heart	UBERON:0002098	36.39	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
endometrium	UBERON:0001295	34.86	gold quality
bone marrow	UBERON:0002371	34.22	gold quality
muscle tissue	UBERON:0002385	33.92	silver quality
primary visual cortex	UBERON:0002436	33.78	gold quality
corpus callosum	UBERON:0002336	33.57	gold quality
mucosa of stomach	UBERON:0001199	33.42	gold quality
vermiform appendix	UBERON:0001154	32.80	silver quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
blood	UBERON:0000178	31.32	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
tonsil	UBERON:0002372	30.83	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	30.79	gold quality
testis	UBERON:0000473	30.59	gold quality
liver	UBERON:0002107	30.50	gold quality
monocyte	CL:0000576	30.47	gold quality
left testis	UBERON:0004533	30.44	silver quality
right testis	UBERON:0004534	30.40	silver quality
gastrocnemius	UBERON:0001388	30.25	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.14

Regulation

Is transcription factor: no

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ctxnd2	ENSMUSG00000105734

Protein

Protein identifiers

Cortexin domain containing 2 — A0A1B0GV90 (reviewed: A0A1B0GV90)

All UniProt accessions (1): A0A1B0GV90

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001371118* (*=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-A0A1B0GV90-F1	80.14	0.48

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 4 (showing top): chr1q21, SIX1_TARGET_GENES, CC2D1A_TARGET_GENES, ZSCAN4_TARGET_GENES

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

22 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CTXND2	C1orf141	Q5JVX7	349
CTXND2	TMEM210	A6NLX4	349
CTXND2	SMIM9	A6NGZ8	347
CTXND2	SMIM8	Q96KF7	304
CTXND2	SLC25A41	Q8N5S1	248
CTXND2	SLC35D1	Q9NTN3	209
CTXND2	CBY2	Q8NA61	205
CTXND2	SLC35D2	Q76EJ3	183
CTXND2	RASEF	Q8IZ41	180
CTXND2	TOMM20L	Q6UXN7	155
CTXND2	TOMM20	Q15388	155

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GQX3, A0A1B0GRQ0, A0A1B0GV90, A4D0T7, A4QNL6, A6NFZ4, A9RA88, B0CMA4, B3DHH5, C0HJJ0, C1PGW0, D3YUK8, F2Z3Y9, F5HFG3, G1TZA0, G2TRP0, O13001, O14068, O39920, P0DKX4, P34535, P57054, P61807, P61808, Q06FW7, Q19443, Q3E8L0, Q3E912, Q3T0S0, Q4V921, Q54L98, Q5F3W2, Q5R687, Q5RBD8, Q5U4Q2, Q66J27, Q6PQZ3, Q80UA9, Q80ZU4, Q8AUU1

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

354 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:150912417:T:C	C35R	0.964
1:150912364:C:A	A17D	0.935
1:150912382:T:G	L23R	0.928
1:150912391:T:G	L26R	0.927
1:150912397:T:G	L28R	0.927
1:150912385:T:G	L24R	0.918
1:150912397:T:C	L28P	0.917
1:150912370:C:A	A19D	0.905
1:150912415:G:C	R34P	0.899
1:150912406:T:G	M31R	0.892
1:150912419:T:G	C35W	0.888
1:150912379:T:A	V22D	0.886
1:150912376:T:A	V21D	0.884
1:150912385:T:C	L24P	0.876
1:150912400:T:A	I29K	0.870
1:150912351:G:C	D13H	0.869
1:150912357:G:C	G15R	0.869
1:150912382:T:A	L23H	0.864
1:150912406:T:A	M31K	0.861
1:150912352:A:T	D13V	0.859
1:150912358:G:A	G15D	0.850
1:150912418:G:A	C35Y	0.850
1:150912420:G:C	A36P	0.849
1:150912363:G:C	A17P	0.848
1:150912372:T:C	F20L	0.830
1:150912374:T:A	F20L	0.830
1:150912374:T:G	F20L	0.830
1:150912427:T:C	L38P	0.827
1:150912400:T:G	I29R	0.822
1:150912391:T:A	L26Q	0.821

dbSNP variants (sampled 300 via entrez): RS1000048275 (1:150901106 T>C), RS1000445602 (1:150897327 A>G), RS1000568984 (1:150889003 C>A,T), RS1000600159 (1:150908261 T>C,G), RS1000625134 (1:150901595 A>G), RS1000699580 (1:150907256 G>A), RS1000702921 (1:150890645 A>C,G), RS1000932089 (1:150897607 C>A), RS1000999532 (1:150902366 C>T), RS1001248075 (1:150889261 G>A), RS1001288629 (1:150900206 T>C), RS1001360504 (1:150896706 A>C,G), RS1001362920 (1:150904120 C>T), RS1001416829 (1:150904478 TA>T), RS1001443079 (1:150901838 A>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs12410394	ARNT, CTXND2		0.00	0

Clinical trials (associated diseases)

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