CEACAM5

CEA cell adhesion molecule 5, the group of V-set domain containing|CD molecules|I-set domain containing|CEA cell adhesion molecule family

Basic information

Region (hg38): 19:41708585-41730433

Previous symbols: [ "CEA" ]

Links

ENSG00000105388 ∙ NCBI:1048 ∙ OMIM:114890 ∙ HGNC:1817 ∙ Uniprot:P06731 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEACAM5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEACAM5 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	6	7
missense			42	6	10	58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	7	16

Variants in CEACAM5

This is a list of pathogenic ClinVar variants found in the CEACAM5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-41708770-C-G		not specified	Uncertain significance (Aug 02, 2021)
19-41709692-C-A		not specified	Uncertain significance (Oct 26, 2022)
19-41709719-A-G		not specified	Uncertain significance (Aug 19, 2021)
19-41709721-C-T		not specified	Uncertain significance (Jan 23, 2023)
19-41709737-C-T		not specified	Uncertain significance (Sep 14, 2023)
19-41709746-A-C		not specified	Uncertain significance (Mar 11, 2025)
19-41709768-G-T			Benign (Dec 28, 2017)
19-41709774-A-C			Benign (Dec 28, 2017)
19-41709825-T-C			Benign (Dec 31, 2019)
19-41709842-A-C		not specified	Uncertain significance (Oct 17, 2024)
19-41709853-A-G			Benign (Dec 31, 2019)
19-41709854-T-C		not specified	Uncertain significance (Dec 05, 2024)
19-41709863-T-C			Benign (Dec 31, 2019)
19-41709878-A-C		not specified	Uncertain significance (Mar 19, 2024)
19-41709886-C-T		not specified	Uncertain significance (Jan 03, 2025)
19-41709901-A-G		not specified	Uncertain significance (Dec 26, 2023)
19-41709911-A-G		not specified	Uncertain significance (Dec 26, 2023)
19-41709914-T-C			Benign (Dec 31, 2019)
19-41709922-C-T			Benign (May 08, 2018)
19-41709949-A-G			Benign (Dec 31, 2019)
19-41709953-T-C			Benign (Dec 31, 2019)
19-41710011-A-T		not specified	Uncertain significance (Mar 11, 2025)
19-41714991-A-G		not specified	Uncertain significance (Feb 12, 2025)
19-41715006-T-G		not specified	Uncertain significance (Mar 04, 2024)
19-41715015-G-A		not specified	Uncertain significance (Nov 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEACAM5	protein_coding	protein_coding	ENST00000221992	9	21215

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.16e-10	0.792	125691	0	56	125747	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.186	370	380	0.973	0.0000210	4543
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000648	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.00144	0.00144
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Intolerance Scores

• loftool: 0.746
• rvis_EVS: 1.92
• rvis_percentile_EVS: 97.44

Haploinsufficiency Scores

• pHI: 0.0483
• hipred: N
• hipred_score: 0.194
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.250

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• 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;negative regulation of apoptotic process;leukocyte migration;negative regulation of anoikis
• Cellular component: extracellular region;plasma membrane;integral component of plasma membrane;cell surface;basolateral plasma membrane;apical plasma membrane;anchored component of membrane;extracellular exosome;integral component of external side of plasma membrane
• Molecular function: GPI anchor binding;identical protein binding;protein homodimerization activity