CDX2
caudal type homeobox 2, the group of HOXL subclass homeoboxes
Basic information
Region (hg38): 13:27960918-27969315
Previous symbols: [ "CDX3" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (43 variants)
- not_provided (3 variants)
- Anorectal_malformation (1 variants)
- Sirenomelia (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDX2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001265.6. 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 | 0 | |||||
| missense | 44 | 45 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 45 | 0 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CDX2 | protein_coding | protein_coding | ENST00000381020 | 3 | 9003 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.529 | 0.468 | 125489 | 0 | 2 | 125491 | 0.00000797 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.06 | 126 | 164 | 0.768 | 0.00000796 | 1963 |
| Missense in Polyphen | 20 | 34.752 | 0.57551 | 417 | ||
| Synonymous | -0.672 | 83 | 75.6 | 1.10 | 0.00000386 | 665 |
| Loss of Function | 2.46 | 2 | 10.7 | 0.187 | 4.62e-7 | 115 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000660 | 0.0000654 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine. Binds preferentially to methylated DNA (PubMed:28473536). {ECO:0000269|PubMed:28473536}.;
- Pathway
- Gastric cancer - Homo sapiens (human);Vitamin D Receptor Pathway;POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation;Preimplantation Embryo;Developmental Biology;POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation;Transcriptional regulation of pluripotent stem cells
(Consensus)
Recessive Scores
- pRec
- 0.551
Intolerance Scores
- loftool
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.32
Haploinsufficiency Scores
- pHI
- 0.900
- hipred
- Y
- hipred_score
- 0.761
- ghis
- 0.408
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.737
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cdx2
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; neoplasm; digestive/alimentary phenotype; limbs/digits/tail phenotype; skeleton 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); normal phenotype; reproductive system phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;blood vessel development;trophectodermal cell differentiation;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;positive regulation of cell population proliferation;endosome to lysosome transport;animal organ morphogenesis;anterior/posterior axis specification;anterior/posterior pattern specification;regulation of somitogenesis;cell differentiation;somatic stem cell population maintenance;establishment or maintenance of epithelial cell apical/basal polarity;positive regulation of cell differentiation;positive regulation of transcription, DNA-templated;intestinal epithelial cell differentiation;labyrinthine layer development
- Cellular component
- condensed nuclear chromosome;nucleus;nucleoplasm;transcriptional repressor complex
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription corepressor activity;methyl-CpG binding