CEACAM3

CEA cell adhesion molecule 3, the group of V-set domain containing|CD molecules|CEA cell adhesion molecule family

Basic information

Region (hg38): 19:41796587-41811554

Previous symbols: [ "CGM1" ]

Links

ENSG00000170956NCBI:1084OMIM:609142HGNC:1815Uniprot:P40198AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • cystic fibrosis (Supportive), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEACAM3 gene.

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
1
clinvar
2
clinvar
3
missense
19
clinvar
5
clinvar
6
clinvar
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)2480055
19-41797658-T-G not specified Uncertain significance (Aug 04, 2023)2616517
19-41797660-G-A not specified Uncertain significance (Jan 27, 2025)3831125
19-41797704-G-C not specified Uncertain significance (Sep 16, 2021)2280379
19-41797721-G-A not specified Likely benign (Jul 05, 2023)2592921
19-41797727-A-G not specified Uncertain significance (Oct 19, 2024)3489868
19-41797753-A-C Benign (Jul 23, 2018)769003
19-41797757-T-A Benign (Jul 23, 2018)769004
19-41797772-T-C Benign (Jul 23, 2018)769005
19-41797774-A-G not specified Likely benign (Dec 07, 2021)2265397
19-41797793-C-T not specified Uncertain significance (May 23, 2024)3265668
19-41797795-C-T not specified Uncertain significance (Dec 10, 2024)3489869
19-41797801-G-C Benign (Jul 13, 2018)769006
19-41797804-G-A not specified Uncertain significance (Feb 22, 2024)3141819
19-41797807-T-A Benign (Jul 13, 2018)769007
19-41797814-G-A not specified Uncertain significance (Oct 10, 2023)3141820
19-41797817-G-A not specified Uncertain significance (May 23, 2023)2510307
19-41797828-T-C not specified Uncertain significance (Jun 03, 2022)2293520
19-41797833-C-A Benign (May 14, 2018)777493
19-41797857-T-C Likely benign (Jul 23, 2018)771930
19-41797893-A-C not specified Uncertain significance (Jan 10, 2025)3831128
19-41797922-A-G Benign (Jul 13, 2018)769008
19-41797929-T-C Benign (Jul 13, 2018)769009
19-41808848-G-A not specified Uncertain significance (Jan 16, 2024)3141821
19-41808863-G-A not specified Uncertain significance (Dec 13, 2022)2334276

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CEACAM3protein_codingprotein_codingENST00000357396 715223
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.07e-90.09491257080351257430.000139
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.07521451421.020.000007971596
Missense in Polyphen3031.190.96184432
Synonymous0.3125659.10.9480.00000361535
Loss of Function0.08371414.30.9768.67e-7139

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005270.000527
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00005360.0000527
Middle Eastern0.000.00
South Asian0.0003770.000327
Other0.0007500.000652

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
neutrophil degranulation;leukocyte migration
Cellular component
plasma membrane;integral component of membrane;specific granule membrane
Molecular function