CFC1
cripto, FRL-1, cryptic family 1
Basic information
Region (hg38): 2:130592165-130599575
Previous symbols: [ "HTX2" ]
Links
Phenotypes
GenCC
Source:
- heterotaxy, visceral, 2, autosomal (Strong), mode of inheritance: AD
- heterotaxy, visceral, 2, autosomal (Strong), mode of inheritance: AD
- heterotaxy, visceral, 2, autosomal (Strong), mode of inheritance: AD
- heterotaxy, visceral, 2, autosomal (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Heterotaxy, visceral, 2, autosomal dominant | AD | Cardiovascular | The condition can involve congenital cardiac anomalies, and awareness may allow early management | Cardiovascular; Gastrointestinal | 11062482; 11562933; 11799476; 18538293 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (19 variants)
- Inborn_genetic_diseases (16 variants)
- not_specified (11 variants)
- Heterotaxy,_visceral,_2,_autosomal (8 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032545.4. 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 | 9 | |||||
| missense | 18 | 28 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 7 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 0 | 25 | 8 | 10 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CFC1 | protein_coding | protein_coding | ENST00000259216 | 6 | 6785 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.105 | 0.785 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.224 | 43 | 39.1 | 1.10 | 0.00000211 | 1370 |
| Missense in Polyphen | 2 | 2.3308 | 0.85806 | 358 | ||
| Synonymous | -0.837 | 25 | 20.2 | 1.24 | 0.00000148 | 447 |
| Loss of Function | 1.24 | 2 | 4.99 | 0.401 | 2.64e-7 | 114 |
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: NODAL coreceptor involved in the correct establishment of the left-right axis. May play a role in mesoderm and/or neural patterning during gastrulation. {ECO:0000269|PubMed:11062482}.;
- Disease
- DISEASE: Heterotaxy, visceral, 2, autosomal (HTX2) [MIM:605376]: A form of visceral heterotaxy, a complex disorder due to disruption of the normal left-right asymmetry of the thoracoabdominal organs. Visceral heterotaxy or situs ambiguus results in randomization of the placement of visceral organs, including the heart, lungs, liver, spleen, and stomach. The organs are oriented randomly with respect to the left-right axis and with respect to one another. It can been associated with variety of congenital defects including cardiac malformations. {ECO:0000269|PubMed:11062482, ECO:0000269|PubMed:11799476}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Developmental Biology;Regulation of signaling by NODAL;Signaling by NODAL
(Consensus)
Recessive Scores
- pRec
- 0.128
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.255
- ghis
- 0.506
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.147
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cfc1
- Phenotype
- digestive/alimentary phenotype; immune system phenotype; liver/biliary system phenotype; respiratory system phenotype; embryo 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); growth/size/body region 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); hematopoietic system phenotype;
Gene ontology
- Biological process
- determination of left/right symmetry;gastrulation;heart development;anterior/posterior pattern specification;BMP signaling pathway;nodal signaling pathway;anatomical structure development
- Cellular component
- cellular_component;extracellular region;plasma membrane;cell surface;anchored component of membrane
- Molecular function
- molecular_function;signaling receptor binding;nodal binding;activin receptor binding