CEACAM4

CEA cell adhesion molecule 4, the group of CEA cell adhesion molecule family|V-set domain containing

Basic information

Region (hg38): 19:41619015-41627074

Previous symbols: [ "CGM7" ]

Links

ENSG00000105352 ∙ NCBI:1089 ∙ OMIM:619159 ∙ HGNC:1816 ∙ Uniprot:O75871 ∙ 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 CEACAM4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEACAM4 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						0
missense			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	0

Variants in CEACAM4

This is a list of pathogenic ClinVar variants found in the CEACAM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-41619337-A-G		not specified	Uncertain significance (Apr 08, 2024)
19-41619340-A-G		not specified	Uncertain significance (Oct 16, 2023)
19-41619356-C-T		not specified	Uncertain significance (Feb 11, 2025)
19-41619680-G-A		not specified	Uncertain significance (Aug 02, 2021)
19-41620595-G-A		not specified	Uncertain significance (Apr 01, 2024)
19-41621694-C-T		not specified	Uncertain significance (Aug 14, 2024)
19-41621742-C-G		not specified	Uncertain significance (Jun 25, 2024)
19-41625631-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-41625637-C-T		not specified	Uncertain significance (Mar 21, 2024)
19-41625646-C-T		not specified	Uncertain significance (Feb 05, 2024)
19-41625651-A-G		not specified	Uncertain significance (May 13, 2024)
19-41625685-G-C		not specified	Uncertain significance (Jan 17, 2024)
19-41625732-C-T		not specified	Uncertain significance (Jun 29, 2023)
19-41625739-T-A		not specified	Uncertain significance (Jun 30, 2023)
19-41625810-G-A		not specified	Uncertain significance (Aug 15, 2023)
19-41625919-A-G		not specified	Likely benign (Jul 30, 2024)
19-41625936-G-A		not specified	Likely benign (Sep 15, 2021)
19-41625939-T-C		not specified	Uncertain significance (Apr 07, 2022)
19-41626939-G-A		not specified	Uncertain significance (Aug 16, 2021)
19-41626957-G-C		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEACAM4	protein_coding	protein_coding	ENST00000221954	7	8099

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.12e-8	0.257	124743	17	961	125721	0.00390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.747	157	133	1.18	0.00000685	1527
Missense in Polyphen		22	19.697	1.1169		278
Synonymous	-0.916	67	58.1	1.15	0.00000347	527
Loss of Function	0.424	12	13.7	0.876	9.36e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0549	0.0541
Ashkenazi Jewish	0.000101	0.0000993
East Asian	0.000220	0.000217
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.000220	0.000217
South Asian	0.000164	0.000163
Other	0.00316	0.00310

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Granulocyte orphan receptor that acts as an trigger efficient phagocytosis of attached particles. {ECO:0000269|PubMed:25567962}.

Recessive Scores

• pRec: 0.0836

Intolerance Scores

• loftool: 0.835
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.92

Haploinsufficiency Scores

• pHI: 0.0535
• hipred: N
• hipred_score: 0.112
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00946

Gene Damage Prediction

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

Gene ontology

• Biological process: phagocytosis
• Cellular component: integral component of plasma membrane;membrane