CEACAM5
protein-codingCEA cell adhesion molecule 5, the group of V-set domain containing|CD molecules|I-set domain containing|CEA cell adhesion molecule family
Gene summary
This gene encodes a cell surface glycoprotein that represents the founding member of the carcinoembryonic antigen (CEA) family of proteins. The encoded protein is used as a clinical biomarker for gastrointestinal cancers and may promote tumor development through its role as a cell adhesion molecule. Additionally, the encoded protein may regulate differentiation, apoptosis, and cell polarity. This gene is present in a CEA family gene cluster on chromosome 19. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]
- CEA
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CEACAM5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004363.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 1 | 5 | 8 | ||
| missense | 93 | 7 | 6 | 106 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 95 | 8 | 11 | 114 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004354.3 | 9 | MANE Select | |
| Ensembl | ENSP00000221992.5 | 9 | MANE Select | |
| RefSeq | NP_001278413.1 | 9 | Standard | |
| RefSeq | NP_001295327.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Post-translational modification: synthesis of GPI-anchored proteins
- Post-translational protein modification
- Metabolism of proteins
- Cell surface interactions at the vascular wall
- Hemostasis
Biological Process
- apoptotic process
- homophilic cell adhesion via plasma membrane adhesion molecules
- heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
- negative regulation of myotube differentiation
- homotypic cell-cell adhesion
Molecular Function
- GPI anchor binding
- identical protein binding
- protein homodimerization activity
Cellular Component
- extracellular region
- plasma membrane
- integral component of plasma membrane
- cell surface
- basolateral plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000221992
- Coding exons
- 9
- Length
- 21215
- Individuals with no LoFs
- 125691
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 56
- Defined
- 125747
- p
- 0.000223
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.186 | 370 | 380 | 0.973 | 0.0000210 | 4543 |
| Missense (PolyPhen) | 104 | 115.81 | 0.89802 | 1598 | ||
| Synonymous | -2.18 | 196 | 161 | 1.22 | 0.00000971 | 1449 |
| Loss of Function | 1.61 | 19 | 28.2 | 0.674 | 0.00000140 | 313 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000065 | 0.000062 | rare |
| South Asian | 0.0014 | 0.0014 | notable |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Cell surface glycoprotein that plays a role in cell adhesion, intracellular signaling and tumor progression (PubMed:2803308, PubMed:10910050, PubMed:10864933). Mediates homophilic and heterophilic cell adhesion with other carcinoembryonic antigen-related cell adhesion molecules, such as CEACAM6 (PubMed:2803308). Plays a role as an oncogene by promoting tumor progression; induces resistance to anoikis of colorectal carcinoma cells (PubMed:10910050). {ECO:0000269|PubMed:10864933, ECO:0000269|PubMed:10910050, ECO:0000269|PubMed:2803308}.;
Intolerance Scores
- LoFtool
- 0.746
- RVIS EVS
- 1.92
- RVIS percentile EVS
- 97.44
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.250
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |