CTBP1
C-terminal binding protein 1
Basic information
Region (hg38): 4:1211445-1250333
Links
Phenotypes
GenCC
Source:
- hypotonia, ataxia, developmental delay, and tooth enamel defect syndrome (Strong), mode of inheritance: AD
- hypotonia, ataxia, developmental delay, and tooth enamel defect syndrome (Strong), mode of inheritance: AD
- hypotonia, ataxia, developmental delay, and tooth enamel defect syndrome (Strong), mode of inheritance: AD
- hypotonia, ataxia, developmental delay, and tooth enamel defect syndrome (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Hypotonia, ataxia, developmental delay, and tooth enamel defect syndrome | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Dental; Neurologic | 27094857 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (271 variants)
- Inborn_genetic_diseases (33 variants)
- Hypotonia,_ataxia,_developmental_delay,_and_tooth_enamel_defect_syndrome (18 variants)
- CTBP1-related_disorder (11 variants)
- not_specified (6 variants)
- 4p_partial_monosomy_syndrome (1 variants)
- Microcephaly (1 variants)
- Intellectual_disability (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTBP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001012614.2. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 89 | 95 | ||||
| missense | 100 | 15 | 116 | |||
| nonsense | 1 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 1 | 0 | 108 | 104 | 4 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CTBP1 | protein_coding | protein_coding | ENST00000290921 | 9 | 38506 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.984 | 0.0156 | 125535 | 0 | 2 | 125537 | 0.00000797 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.31 | 126 | 283 | 0.446 | 0.0000196 | 2799 |
| Missense in Polyphen | 15 | 80.278 | 0.18685 | 813 | ||
| Synonymous | 0.0174 | 133 | 133 | 0.998 | 0.0000107 | 916 |
| Loss of Function | 3.60 | 1 | 17.0 | 0.0587 | 8.99e-7 | 189 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Corepressor targeting diverse transcription regulators such as GLIS2 or BCL6. Has dehydrogenase activity. Involved in controlling the equilibrium between tubular and stacked structures in the Golgi complex. Functions in brown adipose tissue (BAT) differentiation. {ECO:0000269|PubMed:12419229, ECO:0000269|PubMed:15542832, ECO:0000269|PubMed:18212045, ECO:0000269|PubMed:19103759, ECO:0000269|PubMed:9858600}.;
- Disease
- DISEASE: Hypotonia, ataxia, developmental delay, and tooth enamel defect syndrome (HADDTS) [MIM:617915]: An autosomal dominant disorder characterized by delayed motor development, intellectual disability, failure to thrive, hypotonia, ataxia, and tooth enamel defects. {ECO:0000269|PubMed:27094857}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- 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);NOTCH-Ncore;Notch Signaling Pathway;Ectoderm Differentiation;Wnt Signaling Pathway;Pathways Affected in Adenoid Cystic Carcinoma;Wnt Signaling Pathway and Pluripotency;Notch Signaling Pathway;Wnt Signaling Pathway;Degradation of beta-catenin by the destruction complex;Signaling by WNT;Signal Transduction;wnt signaling pathway;Repression of WNT target genes;sumoylation as a mechanism to modulate ctbp-dependent gene responses;EGFR1;Notch signaling pathway;Wnt;Regulation of nuclear beta catenin signaling and target gene transcription;Notch-mediated HES/HEY network;Regulation of retinoblastoma protein;ATM pathway;Regulation of nuclear SMAD2/3 signaling;Presenilin action in Notch and Wnt signaling
(Consensus)
Recessive Scores
- pRec
- 0.387
Intolerance Scores
- loftool
- 0.0645
- rvis_EVS
- -0.74
- rvis_percentile_EVS
- 13.94
Haploinsufficiency Scores
- pHI
- 0.990
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.664
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 | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ctbp1
- Phenotype
- growth/size/body region 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); muscle phenotype; 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); 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); embryo phenotype; skeleton phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;protein phosphorylation;negative regulation of cell population proliferation;viral genome replication;positive regulation of histone deacetylation;negative regulation of histone acetylation;negative regulation of transcription, DNA-templated;white fat cell differentiation;regulation of cell cycle;oxidation-reduction process;negative regulation of histone H4 acetylation
- Cellular component
- nucleus;nucleoplasm;transcription factor complex;transcriptional repressor complex;presynaptic active zone cytoplasmic component;glutamatergic synapse;GABA-ergic synapse
- Molecular function
- DNA-binding transcription factor activity;transcription corepressor activity;protein binding;protein C-terminus binding;transcription factor binding;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;protein domain specific binding;NAD binding;repressing transcription factor binding