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

ENSG00000170956 ∙ NCBI:1084 ∙ OMIM:609142 ∙ HGNC:1815 ∙ Uniprot:P40198 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	2	3
missense			19	5	6	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: gnomAD

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: 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

	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