CEACAM4

protein-coding

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

Gene summary

Predicted to enable protein tyrosine kinase binding activity. Involved in phagocytosis. Predicted to be located in membrane. Predicted to be active in cell surface and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CGM7

MANE transcript

NM_001817.4

Inheritance

—

ClinVar variants

U:41B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr19:41,619,015-41,627,074

External References & Databases

Ensembl (ENSG00000105352)

Transcript & Mutation Effects

hg38 • Region Span ~8.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CEACAM4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 41

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001817.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			38 clinvar	3 clinvar		41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	41	3	0	44

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001817.4	RefSeq	NP_001808.2	7	MANE Select
ENST00000221954.7	Ensembl	ENSP00000221954.2	7	MANE Select
NM_001362492.2	RefSeq	NP_001349421.1	6	Standard
NM_001362493.2	RefSeq	NP_001349422.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

phagocytosis

Cellular Component

integral component of plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000221954
Coding exons: 7
Length: 8099
Individuals with no LoFs: 124743
Homozygous LoFs: 17
Heterozygous LoFs: 961
Defined: 125721
p: 0.00390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.747	157	133	1.18	0.00000685	1527
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.051	0.050	notable
Latino/Admixed American	0.0039	0.0039	notable
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00016	0.00016	rare
Other	0.0032	0.0031	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00946

Gene Damage Prediction

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