CEACAM6

CEA cell adhesion molecule 6, the group of CEA cell adhesion molecule family|V-set domain containing|CD molecules

Basic information

Region (hg38): 19:41750977-41772211

Previous symbols: [ "NCA" ]

Links

ENSG00000086548 ∙ NCBI:4680 ∙ OMIM:163980 ∙ HGNC:1818 ∙ Uniprot:P40199 ∙ 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 CEACAM6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEACAM6 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	1
missense			22	2	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	2

Variants in CEACAM6

This is a list of pathogenic ClinVar variants found in the CEACAM6 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-41755651-T-C		not specified	Uncertain significance (May 24, 2024)
19-41755684-A-G		not specified	Uncertain significance (Mar 29, 2022)
19-41755688-A-T		not specified	Uncertain significance (Jan 31, 2024)
19-41756657-C-T		not specified	Uncertain significance (Dec 16, 2023)
19-41756789-G-A			Benign (Dec 28, 2017)
19-41756810-G-T		not specified	Uncertain significance (Aug 30, 2021)
19-41756842-C-A		not specified	Uncertain significance (Mar 04, 2024)
19-41756842-C-T		not specified	Likely benign (Apr 13, 2022)
19-41756852-C-T		not specified	Uncertain significance (Aug 17, 2022)
19-41756869-G-A		not specified	Uncertain significance (Oct 04, 2022)
19-41756906-T-C		not specified	Uncertain significance (Nov 05, 2021)
19-41756923-G-C		not specified	Uncertain significance (May 05, 2023)
19-41756936-C-T		not specified	Uncertain significance (Dec 21, 2022)
19-41761249-C-T		not specified	Uncertain significance (Oct 29, 2021)
19-41761253-G-C		not specified	Uncertain significance (Jun 07, 2023)
19-41761311-G-A		not specified	Uncertain significance (Jan 20, 2023)
19-41761359-T-A		not specified	Uncertain significance (Jun 18, 2021)
19-41761399-A-T		not specified	Uncertain significance (Feb 15, 2023)
19-41761437-G-A		not specified	Uncertain significance (Jul 26, 2022)
19-41761449-G-A		not specified	Uncertain significance (Jun 18, 2021)
19-41761473-A-G		not specified	Uncertain significance (Dec 16, 2023)
19-41761486-C-T		not specified	Likely benign (Nov 29, 2023)
19-41762013-C-T		not specified	Uncertain significance (Mar 01, 2023)
19-41762045-C-T			Benign (Apr 16, 2018)
19-41762068-A-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEACAM6	protein_coding	protein_coding	ENST00000199764	5	21229

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000119	0.596	125734	0	10	125744	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.188	198	191	1.04	0.0000108	2209
Missense in Polyphen		50	59.007	0.84736		820
Synonymous	-1.07	92	79.9	1.15	0.00000496	725
Loss of Function	0.949	11	15.0	0.735	8.13e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000618	0.0000618
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000575	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000466	0.0000440
Middle Eastern	0.0000575	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface glycoprotein that plays a role in cell adhesion and tumor progression (PubMed:2803308, PubMed:2022629, PubMed:1378450, PubMed:8776764, PubMed:11590190, PubMed:10910050, PubMed:14724575, PubMed:16204051). Intercellular adhesion occurs in a calcium- and fibronectin-independent manner (PubMed:2022629, PubMed:16204051). Mediates homophilic and heterophilic cell adhesion with other carcinoembryonic antigen-related cell adhesion molecules, such as CEACAM5 and CEACAM8 (PubMed:2803308, PubMed:2022629, PubMed:8776764, PubMed:11590190, PubMed:16204051). Heterophilic interaction with CEACAM8 occurs in activated neutrophils (PubMed:8776764). Plays a role in neutrophil adhesion to cytokine-activated endothelial cells (PubMed:1378450). Plays a role as an oncogene by promoting tumor progression; positively regulates cell migration, cell adhesion to endothelial cells and cell invasion (PubMed:16204051). Also involved in the metastatic cascade process by inducing gain resistance to anoikis of pancreatic adenocarcinoma and colorectal carcinoma cells (PubMed:10910050, PubMed:14724575). {ECO:0000269|PubMed:10910050, ECO:0000269|PubMed:11590190, ECO:0000269|PubMed:1378450, ECO:0000269|PubMed:14724575, ECO:0000269|PubMed:16204051, ECO:0000269|PubMed:2022629, ECO:0000269|PubMed:2803308, ECO:0000269|PubMed:8776764}.
• Pathway: Neutrophil degranulation;Extracellular matrix organization;Innate Immune System;Immune System;Fibronectin matrix formation;Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.0690

Intolerance Scores

• loftool: 0.618
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.34

Haploinsufficiency Scores

• pHI: 0.0412
• hipred: N
• hipred_score: 0.278
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.252

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;signal transduction;positive regulation of cell population proliferation;positive regulation of cell migration;positive regulation of heterotypic cell-cell adhesion;neutrophil degranulation;leukocyte migration;positive regulation of endothelial cell-matrix adhesion via fibronectin;negative regulation of anoikis
• Cellular component: extracellular space;plasma membrane;cell surface;apical plasma membrane;anchored component of membrane;azurophil granule membrane
• Molecular function: protein binding;identical protein binding;protein heterodimerization activity