CITED1
Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1
Basic information
Region (hg38): X:72301638-72307187
Previous symbols: [ "MSG1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CITED1 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 | 1 | |||||
| missense | 10 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 10 | 2 | 1 |
Variants in CITED1
This is a list of pathogenic ClinVar variants found in the CITED1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-72301748-G-A | not specified | Uncertain significance (Jul 09, 2021) | ||
| X-72301819-C-T | Benign (Apr 16, 2018) | |||
| X-72301866-T-C | not specified | Uncertain significance (Apr 06, 2024) | ||
| X-72301946-G-A | not specified | Uncertain significance (Mar 07, 2024) | ||
| X-72301950-C-G | not specified | Uncertain significance (Aug 12, 2021) | ||
| X-72301953-C-T | not specified | Uncertain significance (Apr 12, 2024) | ||
| X-72301959-C-T | not specified | Uncertain significance (Apr 19, 2023) | ||
| X-72302043-C-T | not specified | Likely benign (Apr 12, 2022) | ||
| X-72302129-C-T | not specified | Uncertain significance (Oct 12, 2021) | ||
| X-72302147-T-C | not specified | Uncertain significance (Dec 16, 2023) | ||
| X-72302148-T-A | not specified | Uncertain significance (Sep 30, 2022) | ||
| X-72302171-A-G | not specified | Uncertain significance (Jun 01, 2023) | ||
| X-72302821-G-A | not specified | Uncertain significance (Feb 27, 2023) | ||
| X-72302838-A-C | not specified | Uncertain significance (Dec 21, 2021) | ||
| X-72302842-C-T | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| X-72302902-C-T | not specified | Likely benign (Dec 27, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CITED1 | protein_coding | protein_coding | ENST00000453707 | 3 | 5550 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0244 | 0.791 | 118836 | 1 | 1 | 118838 | 0.00000841 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.879 | 64 | 87.1 | 0.735 | 0.00000667 | 1392 |
| Missense in Polyphen | 10 | 25.151 | 0.39761 | 472 | ||
| Synonymous | 0.644 | 35 | 40.2 | 0.871 | 0.00000355 | 470 |
| Loss of Function | 0.982 | 3 | 5.48 | 0.547 | 4.20e-7 | 85 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000384 | 0.0000384 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000135 | 0.00000942 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional coactivator of the p300/CBP-mediated transcription complex. Enhances SMAD-mediated transcription by strengthening the functional link between the DNA-binding SMAD transcription factors and the p300/CBP transcription coactivator complex. Stimulates estrogen-dependent transactivation activity mediated by estrogen receptors signaling; stabilizes the interaction of estrogen receptor ESR1 and histone acetyltransferase EP300. Positively regulates TGF-beta signaling through its association with the SMAD/p300/CBP-mediated transcriptional coactivator complex. Induces transcription from estrogen-responsive promoters and protection against cell death. Potentiates EGR2-mediated transcriptional activation activity from the ERBB2 promoter. Acts as an inhibitor of osteoblastic mineralization through a cAMP-dependent parathyroid hormone receptor signaling. May play a role in pigmentation of melanocytes. Associates with chromatin to the estrogen-responsive TGF-alpha promoter region in a estrogen-dependent manner. {ECO:0000269|PubMed:10722728, ECO:0000269|PubMed:11581164, ECO:0000269|PubMed:21172805}.;
- Pathway
- TGF-beta Signaling Pathway;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;TGF_beta_Receptor;Signaling by Nuclear Receptors;Activation of the TFAP2 (AP-2) family of transcription factors;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors;Estrogen-dependent gene expression;ESR-mediated signaling;Regulation of nuclear SMAD2/3 signaling
(Consensus)
Recessive Scores
- pRec
- 0.150
Intolerance Scores
- loftool
- 0.333
- rvis_EVS
- 0.46
- rvis_percentile_EVS
- 78.28
Haploinsufficiency Scores
- pHI
- 0.395
- hipred
- N
- hipred_score
- 0.459
- ghis
- 0.402
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.811
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cited1
- Phenotype
- endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; embryo phenotype; 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);
Gene ontology
- Biological process
- embryonic axis specification;vasculogenesis;metanephros development;branching involved in ureteric bud morphogenesis;placenta development;negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis;regulation of transcription by RNA polymerase II;nucleocytoplasmic transport;apoptotic process;transforming growth factor beta receptor signaling pathway;brain development;cell population proliferation;positive regulation of gene expression;negative regulation of Wnt signaling pathway;melanocyte differentiation;positive regulation of transforming growth factor beta receptor signaling pathway;response to lipopolysaccharide;response to insulin;response to cytokine;response to interferon-gamma;melanin biosynthetic process;regulation of apoptotic process;pigmentation;negative regulation of neuron apoptotic process;response to estrogen;negative regulation of osteoblast differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;response to cAMP;mesenchymal to epithelial transition;SMAD protein signal transduction;labyrinthine layer development;spongiotrophoblast layer development;response to interleukin-1;response to interleukin-2;response to interleukin-4;response to interleukin-6;response to interleukin-9;response to interleukin-11;response to parathyroid hormone;response to transforming growth factor beta
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol
- Molecular function
- chromatin binding;DNA-binding transcription factor activity;transcription coactivator activity;protein binding;protein C-terminus binding;protein homodimerization activity;transcription regulatory region DNA binding;LBD domain binding;co-SMAD binding