CTBP2

C-terminal binding protein 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 10:124984317-125161170

Links

ENSG00000175029 ∙ NCBI:1488 ∙ OMIM:602619 ∙ HGNC:2495 ∙ Uniprot:P56545 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CTBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTBP2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				14	9	23
missense				9	12	21
nonsense					1	1
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	2	1	6
Total	0	0	3	26	23

Variants in CTBP2

This is a list of pathogenic ClinVar variants found in the CTBP2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-124984870-C-T		not specified	Uncertain significance (Oct 26, 2021)
10-124984873-C-T		not specified	Uncertain significance (Jun 30, 2022)
10-124984936-C-T		not specified	Uncertain significance (Jun 05, 2023)
10-124989578-C-T			Likely benign (May 16, 2018)
10-124989635-G-GA			Uncertain significance (-)
10-124989638-G-T			Likely benign (Aug 01, 2023)
10-124989638-GA-G			Uncertain significance (-)
10-124993224-G-A			Likely benign (Aug 01, 2023)
10-124993263-A-G			Likely benign (Aug 01, 2023)
10-124993299-C-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
10-124993314-C-T			Benign (Dec 26, 2018)
10-124993866-T-C			Likely benign (Aug 01, 2023)
10-124993917-T-C			Likely benign (Sep 01, 2023)
10-124993947-G-A			Likely benign (Sep 01, 2023)
10-124993959-G-A			Likely benign (Aug 01, 2023)
10-124994582-C-T		Pulmonary artery atresia	Pathogenic (-)
10-124997984-G-A		Pulmonary artery atresia	Pathogenic (-)
10-124998037-G-A			Likely benign (Apr 01, 2022)
10-125002969-C-T		Pulmonary artery atresia	Pathogenic (-)
10-125005537-G-A		CTBP2-related disorder	Likely benign (Apr 10, 2019)
10-125005601-C-T		CTBP2-related disorder	Benign (Feb 20, 2019)
10-125005818-G-A		CTBP2-related disorder	Likely benign (Jan 31, 2020)
10-125026072-G-C		CTBP2-related disorder	Benign (Jul 11, 2019)
10-125026145-G-C		CTBP2-related disorder	Benign (Oct 17, 2019)
10-125026149-C-T			Likely benign (May 07, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTBP2	protein_coding	protein_coding	ENST00000309035	9	173319

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00136	0.999	125199	1	546	125746	0.00218

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	581	657	0.884	0.0000442	6240
Missense in Polyphen		166	214.84	0.77267		2087
Synonymous	-1.07	314	291	1.08	0.0000212	2180
Loss of Function	3.79	12	36.8	0.326	0.00000208	366

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00166	0.00165
Ashkenazi Jewish	0.00401	0.00388
East Asian	0.00126	0.00125
Finnish	0.00102	0.00102
European (Non-Finnish)	0.00353	0.00342
Middle Eastern	0.00126	0.00125
South Asian	0.000463	0.000457
Other	0.00197	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Corepressor targeting diverse transcription regulators. Functions in brown adipose tissue (BAT) differentiation (By similarity). {ECO:0000250}.
• Pathway: Chronic myeloid leukemia - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Notch signaling pathway - Homo sapiens (human);Neural Crest Differentiation;Notch Signaling Pathway;Mesodermal Commitment Pathway;Wnt Signaling Pathway and Pluripotency;Notch Signaling Pathway;Wnt Signaling Pathway;Degradation of beta-catenin by the destruction complex;Signaling by WNT;Signal Transduction;Repression of WNT target genes (Consensus)

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.0302
• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.96

Haploinsufficiency Scores

• pHI: 0.482
• hipred: Y
• hipred_score: 0.731
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ctbp2
• Phenotype: muscle phenotype; growth/size/body region phenotype; embryo phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: ctbp2a
• Affected structure: rod bipolar cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: negative regulation of cell population proliferation;synaptic vesicle docking;viral genome replication;positive regulation of chromatin binding;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of retinoic acid receptor signaling pathway;maintenance of presynaptic active zone structure;white fat cell differentiation;oxidation-reduction process;cellular response to leukemia inhibitory factor
• Cellular component: nucleus;transcriptional repressor complex;cell junction;photoreceptor ribbon synapse;presynaptic active zone cytoplasmic component;glutamatergic synapse;GABA-ergic synapse;presynaptic cytosol
• Molecular function: chromatin binding;transcription coactivator activity;transcription corepressor activity;protein binding;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;protein kinase binding;retinoic acid receptor binding;protein-containing complex binding;NAD binding;structural constituent of presynaptic active zone