CXXC1
Basic information
Region (hg38): 18:50282343-50287839
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (63 variants)
- not_provided (9 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXXC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014593.4. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | |||||
| missense | 64 | 64 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 65 | 2 | 4 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CXXC1 | protein_coding | protein_coding | ENST00000412036 | 15 | 5962 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.895 | 0.105 | 125739 | 0 | 9 | 125748 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.15 | 256 | 442 | 0.579 | 0.0000325 | 4289 |
| Missense in Polyphen | 73 | 217 | 0.3364 | 2161 | ||
| Synonymous | -1.14 | 182 | 163 | 1.11 | 0.0000102 | 1274 |
| Loss of Function | 4.67 | 7 | 38.1 | 0.183 | 0.00000201 | 433 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000906 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000361 | 0.0000352 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional activator that exhibits a unique DNA binding specificity for CpG unmethylated motifs with a preference for CpGG. {ECO:0000269|PubMed:21407193}.;
- Pathway
- XBP1(S) activates chaperone genes
(Consensus)
Recessive Scores
- pRec
- 0.116
Intolerance Scores
- loftool
- 0.286
- rvis_EVS
- -0.93
- rvis_percentile_EVS
- 9.47
Haploinsufficiency Scores
- pHI
- 0.145
- hipred
- Y
- hipred_score
- 0.704
- ghis
- 0.653
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.994
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cxxc1
- Phenotype
- reproductive system 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); embryo phenotype;
Zebrafish Information Network
- Gene name
- cxxc1b
- Affected structure
- blood vasculature
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;IRE1-mediated unfolded protein response;positive regulation of transcription, DNA-templated;histone H3-K4 methylation
- Cellular component
- nucleus;nucleoplasm;cytosol;nuclear matrix;nuclear speck;histone methyltransferase complex;Set1C/COMPASS complex
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;protein binding;zinc ion binding;histone methyltransferase activity (H3-K4 specific);unmethylated CpG binding