CEACAM3
Basic information
Region (hg38): 19:41796587-41811554
Previous symbols: [ "CGM1" ]
Links
Phenotypes
GenCC
Source:
- cystic fibrosis (Supportive), mode of inheritance: AR
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 CEACAM3 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 | 3 | |||||
missense | 19 | 30 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 19 | 6 | 8 |
Variants in CEACAM3
This is a list of pathogenic ClinVar variants found in the CEACAM3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
19-41796711-T-C | not specified | Uncertain significance (Jan 31, 2023) | ||
19-41797658-T-G | not specified | Uncertain significance (Aug 04, 2023) | ||
19-41797660-G-A | not specified | Uncertain significance (Jan 27, 2025) | ||
19-41797704-G-C | not specified | Uncertain significance (Sep 16, 2021) | ||
19-41797721-G-A | not specified | Likely benign (Jul 05, 2023) | ||
19-41797727-A-G | not specified | Uncertain significance (Oct 19, 2024) | ||
19-41797753-A-C | Benign (Jul 23, 2018) | |||
19-41797757-T-A | Benign (Jul 23, 2018) | |||
19-41797772-T-C | Benign (Jul 23, 2018) | |||
19-41797774-A-G | not specified | Likely benign (Dec 07, 2021) | ||
19-41797793-C-T | not specified | Uncertain significance (May 23, 2024) | ||
19-41797795-C-T | not specified | Uncertain significance (Dec 10, 2024) | ||
19-41797801-G-C | Benign (Jul 13, 2018) | |||
19-41797804-G-A | not specified | Uncertain significance (Feb 22, 2024) | ||
19-41797807-T-A | Benign (Jul 13, 2018) | |||
19-41797814-G-A | not specified | Uncertain significance (Oct 10, 2023) | ||
19-41797817-G-A | not specified | Uncertain significance (May 23, 2023) | ||
19-41797828-T-C | not specified | Uncertain significance (Jun 03, 2022) | ||
19-41797833-C-A | Benign (May 14, 2018) | |||
19-41797857-T-C | Likely benign (Jul 23, 2018) | |||
19-41797893-A-C | not specified | Uncertain significance (Jan 10, 2025) | ||
19-41797922-A-G | Benign (Jul 13, 2018) | |||
19-41797929-T-C | Benign (Jul 13, 2018) | |||
19-41808848-G-A | not specified | Uncertain significance (Jan 16, 2024) | ||
19-41808863-G-A | not specified | Uncertain significance (Dec 13, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CEACAM3 | protein_coding | protein_coding | ENST00000357396 | 7 | 15223 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.07e-9 | 0.0949 | 125708 | 0 | 35 | 125743 | 0.000139 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.0752 | 145 | 142 | 1.02 | 0.00000797 | 1596 |
Missense in Polyphen | 30 | 31.19 | 0.96184 | 432 | ||
Synonymous | 0.312 | 56 | 59.1 | 0.948 | 0.00000361 | 535 |
Loss of Function | 0.0837 | 14 | 14.3 | 0.976 | 8.67e-7 | 139 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000527 | 0.000527 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000536 | 0.0000527 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000377 | 0.000327 |
Other | 0.000750 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Major granulocyte receptor mediating recognition and efficient opsonin-independent phagocytosis of CEACAM-binding microorganisms, including Neissiria, Moxarella and Haemophilus species, thus playing an important role in the clearance of pathogens by the innate immune system. Responsible for RAC1 stimulation in the course of pathogen phagocytosis. {ECO:0000269|PubMed:12864848, ECO:0000269|PubMed:14707113}.;
- Pathway
- Neutrophil degranulation;Innate Immune System;Immune System;Cell surface interactions at the vascular wall;Hemostasis
(Consensus)
Intolerance Scores
- loftool
- 0.811
- rvis_EVS
- 0.42
- rvis_percentile_EVS
- 76.96
Haploinsufficiency Scores
- pHI
- 0.0683
- hipred
- N
- hipred_score
- 0.139
- ghis
- 0.462
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.00197
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- neutrophil degranulation;leukocyte migration
- Cellular component
- plasma membrane;integral component of membrane;specific granule membrane
- Molecular function