CER1
cerberus 1, DAN family BMP antagonist, the group of DAN family
Basic information
Region (hg38): 9:14719724-14722733
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 CER1 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 | 13 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 3 | 0 |
Variants in CER1
This is a list of pathogenic ClinVar variants found in the CER1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-14720162-C-G | not specified | Uncertain significance (Sep 27, 2022) | ||
| 9-14720298-G-A | not specified | Uncertain significance (Mar 14, 2023) | ||
| 9-14720298-G-C | not specified | Uncertain significance (May 20, 2024) | ||
| 9-14720337-C-T | not specified | Uncertain significance (May 17, 2023) | ||
| 9-14720352-A-G | not specified | Uncertain significance (May 15, 2024) | ||
| 9-14722293-C-T | not specified | Likely benign (Jan 22, 2024) | ||
| 9-14722330-G-A | not specified | Uncertain significance (Apr 19, 2023) | ||
| 9-14722381-T-C | not specified | Uncertain significance (Nov 09, 2023) | ||
| 9-14722473-C-T | not specified | Uncertain significance (Dec 18, 2023) | ||
| 9-14722487-G-T | not specified | Uncertain significance (Aug 16, 2022) | ||
| 9-14722498-C-T | not specified | Uncertain significance (Nov 10, 2022) | ||
| 9-14722499-G-A | Likely benign (Jul 01, 2022) | |||
| 9-14722539-C-T | not specified | Uncertain significance (Oct 29, 2021) | ||
| 9-14722542-G-A | not specified | Uncertain significance (Jun 11, 2021) | ||
| 9-14722560-T-C | not specified | Likely benign (Feb 16, 2023) | ||
| 9-14722566-G-C | not specified | Uncertain significance (Oct 10, 2023) | ||
| 9-14722576-C-T | not specified | Uncertain significance (Feb 06, 2024) | ||
| 9-14722596-T-A | not specified | Uncertain significance (Mar 20, 2024) | ||
| 9-14722602-C-T | not specified | Uncertain significance (Apr 12, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CER1 | protein_coding | protein_coding | ENST00000380911 | 2 | 2994 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000167 | 0.262 | 125714 | 0 | 33 | 125747 | 0.000131 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.64 | 203 | 147 | 1.38 | 0.00000746 | 1764 |
| Missense in Polyphen | 39 | 41.936 | 0.92999 | 561 | ||
| Synonymous | -1.55 | 74 | 58.9 | 1.26 | 0.00000334 | 527 |
| Loss of Function | -0.152 | 7 | 6.58 | 1.06 | 2.79e-7 | 86 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00111 | 0.00109 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000167 | 0.000167 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000655 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cytokine that may play a role in anterior neural induction and somite formation during embryogenesis in part through a BMP-inhibitory mechanism. Can regulate Nodal signaling during gastrulation as well as the formation and patterning of the primitive streak (By similarity). {ECO:0000250}.;
- Pathway
- Wnt signaling pathway - Homo sapiens (human);Endoderm Differentiation;Wnt Signaling Pathway;Developmental Biology;Regulation of signaling by NODAL;Signal Transduction;Signaling by NODAL;BMP receptor signaling;BMP Signalling Pathway;Signaling by BMP;Signaling by TGF-beta family members
(Consensus)
Recessive Scores
- pRec
- 0.157
Intolerance Scores
- loftool
- 0.608
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.61
Haploinsufficiency Scores
- pHI
- 0.332
- hipred
- N
- hipred_score
- 0.123
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0414
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cer1
- Phenotype
- skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail 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); normal phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); craniofacial phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- ureteric bud development;growth plate cartilage chondrocyte proliferation;gastrulation;nervous system development;negative regulation of cell population proliferation;anterior/posterior axis specification;anterior/posterior pattern specification;regulation of signaling receptor activity;signal transduction involved in regulation of gene expression;negative regulation of Wnt signaling pathway;bone mineralization;BMP signaling pathway;negative regulation of BMP signaling pathway;negative regulation of activin receptor signaling pathway;sequestering of BMP in extracellular matrix;cell migration involved in gastrulation;determination of dorsal identity;determination of heart left/right asymmetry;cellular response to BMP stimulus;negative regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry;negative regulation of mesoderm development
- Cellular component
- extracellular region;extracellular space
- Molecular function
- cytokine activity;morphogen activity;BMP binding;protein homodimerization activity