CEACAM7

protein-coding

CEA cell adhesion molecule 7, the group of V-set domain containing|CEA cell adhesion molecule family

Gene summary

This gene encodes a cell surface glycoprotein and member of the carcinoembryonic antigen (CEA) family of proteins. Expression of this gene may be downregulated in colon and rectal cancer. Additionally, lower expression levels of this gene may be predictive of rectal cancer recurrence. This gene is present in a CEA family gene cluster on chromosome 19. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

Previous symbols:

CGM2

MANE transcript

NM_001291485.2

Inheritance

—

ClinVar variants

U:43B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr19:41,673,303-41,706,976

External References & Databases

Ensembl (ENSG00000007306)

Transcript & Mutation Effects

hg38 • Region Span ~33.7 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 CEACAM7 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 44

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001291485.2. 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 clinvar		2
missense			42 clinvar	2 clinvar		44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	3	0	46

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001291485.2	RefSeq	NP_001278414.1	4	MANE Select
ENST00000401731.6	Ensembl	ENSP00000385932.1	4	MANE Select
NM_006890.5	RefSeq	NP_008821.2	4	Standard
ENST00000006724.7	Ensembl	ENSP00000006724.3	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational modification: synthesis of GPI-anchored proteins
Post-translational protein modification
Metabolism of proteins

Cellular Component

extracellular region
plasma membrane
apical plasma membrane
anchored component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000006724
Coding exons: 4
Length: 33661
Individuals with no LoFs: 125138
Homozygous LoFs: 1
Heterozygous LoFs: 602
Defined: 125741
p: 0.00240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.637	172	150	1.15	0.00000811	1711
Missense (PolyPhen)		57	44.305	1.2865		577
Synonymous	-0.192	64	62.1	1.03	0.00000372	538
Loss of Function	0.227	11	11.8	0.929	6.36e-7	125

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00056	0.00055	rare
Latino/Admixed American	0.00074	0.00072	rare
Ashkenazi Jewish	0.0066	0.0066	notable
East Asian	0.00033	0.00033	rare
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.0035	0.0035	notable
South Asian	0.0027	0.0027	notable
Other	0.0023	0.0023	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.849
RVIS EVS: 0.97
RVIS percentile EVS: 90.34

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0997

Gene Damage Prediction

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