CXXC5
Basic information
Region (hg38): 5:139647299-139683882
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (39 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXXC5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016463.9. 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 | 1 | |||||
| missense | 36 | 39 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 36 | 4 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CXXC5 | protein_coding | protein_coding | ENST00000302517 | 2 | 36584 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.889 | 0.110 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.58 | 157 | 223 | 0.703 | 0.0000155 | 2102 |
| Missense in Polyphen | 34 | 73.653 | 0.46162 | 678 | ||
| Synonymous | 0.607 | 90 | 97.6 | 0.922 | 0.00000773 | 682 |
| Loss of Function | 2.47 | 0 | 7.13 | 0.00 | 3.70e-7 | 85 |
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 | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May indirectly participate in activation of the NF- kappa-B and MAPK pathways. Acts as a mediator of BMP4-mediated modulation of canonical Wnt signaling activity in neural stem cells (By similarity). Required for DNA damage-induced ATM phosphorylation, p53 activation and cell cycle arrest. Involved in myelopoiesis. Transcription factor. Binds to the oxygen responsive element of COX4I2 and represses its transcription under hypoxia conditions (4% oxygen), as well as normoxia conditions (20% oxygen) (PubMed:23303788). May repress COX4I2 transactivation induced by CHCHD2 and RBPJ (PubMed:23303788). {ECO:0000250, ECO:0000269|PubMed:19182210, ECO:0000269|PubMed:19557330, ECO:0000269|PubMed:23303788}.;
- Pathway
- Signal Transduction;Signaling by Nuclear Receptors;Estrogen-dependent gene expression;ESR-mediated signaling
(Consensus)
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- loftool
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- 0.441
- hipred
- Y
- hipred_score
- 0.593
- ghis
- 0.618
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.927
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cxxc5
- Phenotype
- limbs/digits/tail phenotype; skeleton phenotype; cellular phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- cxxc5a
- Affected structure
- caudal vein plexus
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;positive regulation of I-kappaB kinase/NF-kappaB signaling
- Cellular component
- nucleoplasm;cytosol
- Molecular function
- protein binding;transcription factor binding;zinc ion binding;sequence-specific DNA binding