GeneBe

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.

  • not_provided (26 variants)
  • CTBP2-related_disorder (24 variants)
  • Pulmonary_artery_atresia (4 variants)
  • EBV-positive_nodal_T-_and_NK-cell_lymphoma (2 variants)
  • not_specified (1 variants)

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. These statistics are base on transcript: NM_000001329.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
10
clinvar
1
clinvar
 11
missense
3
clinvar
 3
nonsense
1
clinvar
1
clinvar
 2
start loss
0
frameshift
2
clinvar
 2
splice donor/acceptor (+/-2bp)
0
Total 3 0 2 11 2

Highest pathogenic variant AF is 0.000019208

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CTBP2protein_codingprotein_codingENST00000309035 9173319
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.001360.99912519915461257460.00218
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.065816570.8840.00004426240
Missense in Polyphen166214.840.772672087
Synonymous-1.073142911.080.00002122180
Loss of Function3.791236.80.3260.00000208366

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001660.00165
Ashkenazi Jewish0.004010.00388
East Asian0.001260.00125
Finnish0.001020.00102
European (Non-Finnish)0.003530.00342
Middle Eastern0.001260.00125
South Asian0.0004630.000457
Other0.001970.00196

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

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

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