CTNND2 (catenin delta 2)

Gene

• Entrez ID: 1501
• Gene name: Catenin delta 2
• Gene symbol: CTNND2
• Synonyms (NCBI Gene): GT24, NPRAP
• Chromosome: 5
• Chromosome location: 5p15.2
• Summary: This gene encodes an adhesive junction associated protein of the armadillo/beta-catenin superfamily and is implicated in brain and eye development and cancer formation. The protein encoded by this gene promotes the disruption of E-cadherin based adherens

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs886041494	G>A,C	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant, stop gained
rs1057518120	T>C	Likely-pathogenic	Genic upstream transcript variant, missense variant, coding sequence variant, 5 prime UTR variant, intron variant
rs1064796494	G>T	Likely-pathogenic	Genic upstream transcript variant, upstream transcript variant, stop gained, coding sequence variant, intron variant
rs1554008611	T>C	Likely-pathogenic	Splice acceptor variant
rs1554046915	T>A	Likely-pathogenic	Coding sequence variant, 5 prime UTR variant, stop gained, intron variant
rs1561136548	C>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs1580669869	->CC	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant, 5 prime UTR variant
rs1581078962	C>-	Likely-pathogenic	Genic upstream transcript variant, upstream transcript variant, coding sequence variant, frameshift variant, intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT735742	hsa-miR-218-5p	Luciferase reporter assay, Western blotting, qRT-PCR	31520422
MIRT915178	hsa-miR-1286	CLIP-seq
MIRT915179	hsa-miR-218	CLIP-seq
MIRT915180	hsa-miR-23a	CLIP-seq
MIRT915181	hsa-miR-23b	CLIP-seq
MIRT915182	hsa-miR-23c	CLIP-seq
MIRT915183	hsa-miR-3074-3p	CLIP-seq
MIRT915184	hsa-miR-337-3p	CLIP-seq
MIRT915185	hsa-miR-3607-3p	CLIP-seq
MIRT915186	hsa-miR-3614-3p	CLIP-seq
MIRT915187	hsa-miR-3667-3p	CLIP-seq
MIRT915188	hsa-miR-3671	CLIP-seq
MIRT915189	hsa-miR-3686	CLIP-seq
MIRT915190	hsa-miR-3688-3p	CLIP-seq
MIRT915191	hsa-miR-3691-5p	CLIP-seq
MIRT915192	hsa-miR-4297	CLIP-seq
MIRT915193	hsa-miR-431	CLIP-seq
MIRT915194	hsa-miR-4438	CLIP-seq
MIRT915195	hsa-miR-4652-3p	CLIP-seq
MIRT915196	hsa-miR-4659a-3p	CLIP-seq
MIRT915197	hsa-miR-4659b-3p	CLIP-seq
MIRT915198	hsa-miR-4711-3p	CLIP-seq
MIRT915199	hsa-miR-4719	CLIP-seq
MIRT915200	hsa-miR-4720-3p	CLIP-seq
MIRT915201	hsa-miR-4722-5p	CLIP-seq
MIRT915202	hsa-miR-4731-3p	CLIP-seq
MIRT915203	hsa-miR-4752	CLIP-seq
MIRT915204	hsa-miR-4768-3p	CLIP-seq
MIRT915205	hsa-miR-4778-3p	CLIP-seq
MIRT915206	hsa-miR-4778-5p	CLIP-seq
MIRT915207	hsa-miR-4801	CLIP-seq
MIRT915208	hsa-miR-4804-3p	CLIP-seq
MIRT915209	hsa-miR-495	CLIP-seq
MIRT915210	hsa-miR-499-3p	CLIP-seq
MIRT915211	hsa-miR-499a-3p	CLIP-seq
MIRT915212	hsa-miR-513a-3p	CLIP-seq
MIRT915213	hsa-miR-523	CLIP-seq
MIRT915214	hsa-miR-581	CLIP-seq
MIRT915215	hsa-miR-586	CLIP-seq
MIRT915216	hsa-miR-636	CLIP-seq
MIRT1971449	hsa-miR-1203	CLIP-seq
MIRT1971450	hsa-miR-1208	CLIP-seq
MIRT1971451	hsa-miR-1279	CLIP-seq
MIRT915180	hsa-miR-23a	CLIP-seq
MIRT915181	hsa-miR-23b	CLIP-seq
MIRT915182	hsa-miR-23c	CLIP-seq
MIRT915183	hsa-miR-3074-3p	CLIP-seq
MIRT1971452	hsa-miR-3160-5p	CLIP-seq
MIRT1971453	hsa-miR-339-3p	CLIP-seq
MIRT1971454	hsa-miR-361-5p	CLIP-seq
MIRT1971455	hsa-miR-3691-3p	CLIP-seq
MIRT1971456	hsa-miR-4307	CLIP-seq
MIRT1971457	hsa-miR-4661-3p	CLIP-seq
MIRT915199	hsa-miR-4719	CLIP-seq
MIRT915202	hsa-miR-4731-3p	CLIP-seq
MIRT915207	hsa-miR-4801	CLIP-seq
MIRT915215	hsa-miR-586	CLIP-seq
MIRT1971458	hsa-miR-651	CLIP-seq
MIRT2207151	hsa-miR-1297	CLIP-seq
MIRT2207152	hsa-miR-141	CLIP-seq
MIRT2207153	hsa-miR-200a	CLIP-seq
MIRT2207154	hsa-miR-200b	CLIP-seq
MIRT2207155	hsa-miR-200c	CLIP-seq
MIRT915180	hsa-miR-23a	CLIP-seq
MIRT915181	hsa-miR-23b	CLIP-seq
MIRT915182	hsa-miR-23c	CLIP-seq
MIRT2207156	hsa-miR-26a	CLIP-seq
MIRT2207157	hsa-miR-26b	CLIP-seq
MIRT915183	hsa-miR-3074-3p	CLIP-seq
MIRT2207158	hsa-miR-3125	CLIP-seq
MIRT1971452	hsa-miR-3160-5p	CLIP-seq
MIRT1971454	hsa-miR-361-5p	CLIP-seq
MIRT1971455	hsa-miR-3691-3p	CLIP-seq
MIRT915191	hsa-miR-3691-5p	CLIP-seq
MIRT2207159	hsa-miR-3914	CLIP-seq
MIRT2207160	hsa-miR-3916	CLIP-seq
MIRT2207161	hsa-miR-3928	CLIP-seq
MIRT2207162	hsa-miR-429	CLIP-seq
MIRT2207163	hsa-miR-4465	CLIP-seq
MIRT915195	hsa-miR-4652-3p	CLIP-seq
MIRT1971457	hsa-miR-4661-3p	CLIP-seq
MIRT2207164	hsa-miR-4718	CLIP-seq
MIRT915199	hsa-miR-4719	CLIP-seq
MIRT2207165	hsa-miR-4729	CLIP-seq
MIRT915203	hsa-miR-4752	CLIP-seq
MIRT2207166	hsa-miR-4797-5p	CLIP-seq
MIRT2207167	hsa-miR-494	CLIP-seq
MIRT2207168	hsa-miR-579	CLIP-seq
MIRT915215	hsa-miR-586	CLIP-seq
MIRT1971458	hsa-miR-651	CLIP-seq
MIRT2207169	hsa-miR-664	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	19706605, 19706687, 22022388, 24550280, 25009281, 30126976
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	TAS	9342840
GO:0005886	Component	Plasma membrane	IBA
GO:0005912	Component	Adherens junction	IBA
GO:0005912	Component	Adherens junction	IEA
GO:0007155	Process	Cell adhesion	IEA
GO:0007155	Process	Cell adhesion	TAS	9223106
GO:0007165	Process	Signal transduction	TAS	9223106
GO:0008013	Function	Beta-catenin binding	IPI	25807484
GO:0014069	Component	Postsynaptic density	IBA
GO:0016055	Process	Wnt signaling pathway	IEA
GO:0030425	Component	Dendrite	IEA
GO:0042995	Component	Cell projection	IEA
GO:0043204	Component	Perikaryon	IDA	22022388
GO:0043204	Component	Perikaryon	IEA
GO:0045296	Function	Cadherin binding	IBA
GO:0050808	Process	Synapse organization	IMP	25807484
GO:0060828	Process	Regulation of canonical Wnt signaling pathway	IMP	25807484
GO:0060997	Process	Dendritic spine morphogenesis	IBA
GO:0060997	Process	Dendritic spine morphogenesis	IMP	25807484
GO:0070161	Component	Anchoring junction	IEA
GO:0098609	Process	Cell-cell adhesion	IBA
GO:0098609	Process	Cell-cell adhesion	IEA

Other IDs

• MIM: 604275
• HGNC: 2516
• e!Ensembl: ENSG00000169862

Protein

• UniProt ID: Q9UQB3
• Protein name: Catenin delta-2 (Delta-catenin) (GT24) (Neural plakophilin-related ARM-repeat protein) (NPRAP) (Neurojungin)
• Protein function: Has a critical role in neuronal development, particularly in the formation and/or maintenance of dendritic spines and synapses (PubMed:25807484). Involved in the regulation of Wnt signaling (PubMed:25807484). It probably acts on beta-catenin tur
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00514	Arm	581 → 621	Armadillo/beta-catenin-like repeat	Repeat
  PF00514	Arm	625 → 666	Armadillo/beta-catenin-like repeat	Repeat
  PF00514	Arm	834 → 875	Armadillo/beta-catenin-like repeat	Repeat
  PF00514	Arm	882 → 921	Armadillo/beta-catenin-like repeat	Repeat

• Tissue specificity: TISSUE SPECIFICITY: Expressed in brain; highest expression is observed in fetal brain (PubMed:25807484). {ECO:0000269|PubMed:25807484}.
• Sequence:

  MFARKPPGAAPLGAMPVPDQPSSASEKTSSLSPGLNTSNGDGSETETTSAILASVKEQEL
  QFERLTRELEAERQIVASQLERCKLGSETGSMSSMSSAEEQFQWQSQDGQKDIEDELTTG
  LELVDSCIRSLQESGILDPQDYSTGERPSLLSQSALQLNSKPEGSFQYPASYHSNQTLAL
  GETTPSQLPARGTQARATGQSFSQGTTSRAGHLAGPEPAPPPPPPPREPFAPSLGSAFHL
  PDAPPAAAAAALYYSSSTLPAPPRGGSPLAAPQGGSPTKLQRGGSAPEGATYAAPRGSSP
  KQSPSRLAKSYSTSSPINIVVSSAGLSPIRVTSPPTVQSTISSSPIHQLSSTIGTYATLS
  PTKRLVHASEQYSKHSQELYATATLQRPGSLAAGSRASYSSQHGHLGPELRALQSPEHHI
  DPIYEDRVYQKPPMRSLSQSQGDPLPPAHTGTYRTSTAPSSPGVDSVPLQRTGSQHGPQN
  AAAATFQRASYAAGPASNYADPYRQLQYCPSVESPYSKSGPALPPEGTLARSPSIDSIQK
  DPREFGWRDPELPEVIQMLQHQFPSVQSNAAAYLQHLCFGDNKIKAEIRRQGGIQLLVDL
  LDHRMTEVHRSACGALRNLVYGKANDDNKIALKNCGGIPALVRLLRKTTDLEIRELVTGV
  LWNLSSCDALKMPIIQDALAVLTNAVIIPHSGWENSPLQDDRKIQLHSSQVLRNATGCLR
  NVSSAGEEARRRMRECDGLTDALLYVIQSALGSSEIDSKTVENCVCILRNLSYRLAAETS
  QGQHMGTDELDGLLCGEANGKDAESSGCWGKKKKKKKSQDQWDGVGPLPDCAEPPKGIQM
  LWHPSIVKPYLTLLSECSNPDTLEGAAGALQNLAAGSWKWSVYIRAAVRKEKGLPILVEL
  LRIDNDRVVCAVATALRNMALDVRNKELIGKYAMRDLVHRLPGGNNSNNTASKAMSDDTV
  TAVCCTLHEVITKNMENAKALRDAGGIEKLVGISKSKGDKHSPKVVKAASQVLNSMWQYR
  DLRSLYKKDGWSQYHFVASSSTIERDRQRPYSSSRTPSISPVRVSPNNRSASAPASPREM
  ISLKERKTDYECTGSNATYHGAKGEHTSRKDAMTAQNTGISTLYRNSYGAPAEDIKHNQV
  SAQPVPQEPSRKDYETYQPFQNSTRNYDESFFEDQVHHRPPASEYTMHLGLKSTGNYVDF
  YSAARPYSELNYETSHYPASPDSWV

• Sequence length: 1225

Pathways

KEGG:

Wnt signaling pathway

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
CTNND2-related disorder	Likely pathogenic	rs2546872978	RCV003402431

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Cholangiocarcinoma	Benign	rs4466167	RCV005919741
CTNND2-associated Neurodevelopmental syndrome	Uncertain significance	rs781743390, rs2149799429	RCV002275589 RCV002275590
Hepatocellular carcinoma	Benign	rs2302179	RCV005919735
Malignant lymphoma, large B-cell, diffuse	Benign	rs2302179	RCV005919736
Malignant tumor of urinary bladder	Benign; Likely benign	rs150306957	RCV005918712
Neurodevelopmental disorder	Conflicting classifications of pathogenicity	rs1016219246, rs886041494	RCV002272494 RCV003389050
Ovarian serous cystadenocarcinoma	Benign	rs111573890	RCV005918631
Sarcoma	Benign	rs13161964	RCV005924540
Uterine carcinosarcoma	Benign	rs4466167	RCV005919740
Uterine corpus endometrial carcinoma	Benign; Likely benign	rs111573890, rs149766664, rs201041399	RCV005918632 RCV005923514 RCV005920880

Associations from Text Mining
Disease Name	Relationship Type	References
Adenocarcinoma	Associate	18978817, 35164838
Adenocarcinoma of Lung	Associate	32672359
Alzheimer Disease	Associate	22022388, 22984439
Anxiety	Associate	34236339
Anxiety Disorders	Associate	24256404
Autism Spectrum Disorder	Associate	25106414
Barrett Esophagus	Associate	35164838
Carcinoma Hepatocellular	Associate	24966965
Cataract	Associate	22984439
Cataract Age Related Nuclear	Associate	22984439
Cerebral Palsy	Associate	23695280
Cri du Chat Syndrome	Associate	22022388, 24677774, 33517598
Depressive Disorder	Associate	32681239
Depressive Disorder Major	Associate	24256404
Down Syndrome	Associate	40667715
Dyslexia	Associate	28839234
Esophageal Squamous Cell Carcinoma	Associate	21734802, 30880778
Glioblastoma	Associate	23917401
Glioma	Associate	23917401
HIV Infections	Associate	29206233
Insulin Resistance	Associate	31208038
Intellectual Disability	Associate	22022388
Learning Disabilities	Associate	25106414
Mental Disorders	Associate	24256404
Myopia	Associate	21095009, 36945837
Neoplasm Metastasis	Associate	24966965
Neoplasms	Associate	18978817, 22151302, 25154973
Pain	Associate	32681239, 34236339
Pancreatitis	Associate	34236339
Prostatic Neoplasms	Associate	18978817
Retinal Hemorrhage	Associate	33517598
Schizophrenia	Associate	24256404