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.

• not_specified (38 variants)
• not_provided (9 variants)

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. These statistics are base on transcript: NM_000001815.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			31	7	6	44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	8	8

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