CEACAM7

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

Basic information

Region (hg38): 19:41673303-41706976

Previous symbols: [ "CGM2" ]

Links

ENSG00000007306 ∙ NCBI:1087 ∙ OMIM:619160 ∙ HGNC:1819 ∙ Uniprot:Q14002 ∙ 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 CEACAM7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEACAM7 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in CEACAM7

This is a list of pathogenic ClinVar variants found in the CEACAM7 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-41677459-C-T		not specified	Uncertain significance (Oct 11, 2024)
19-41677500-T-A		not specified	Uncertain significance (Oct 01, 2024)
19-41683787-C-T		not specified	Uncertain significance (Apr 24, 2024)
19-41683815-G-A		not specified	Uncertain significance (Dec 28, 2023)
19-41683850-T-C		not specified	Uncertain significance (Apr 09, 2024)
19-41683859-A-G		not specified	Likely benign (Aug 14, 2024)
19-41683976-G-A		not specified	Uncertain significance (Oct 07, 2024)
19-41683989-A-C		not specified	Uncertain significance (May 29, 2024)
19-41683997-A-G		not specified	Likely benign (Feb 11, 2022)
19-41684024-T-C		not specified	Uncertain significance (May 05, 2022)
19-41686913-C-T		not specified	Uncertain significance (Mar 19, 2024)
19-41686921-G-T		not specified	Uncertain significance (Nov 09, 2022)
19-41686955-G-T		not specified	Uncertain significance (Dec 13, 2022)
19-41686982-T-C		not specified	Uncertain significance (Feb 21, 2024)
19-41686999-T-A		not specified	Uncertain significance (Apr 29, 2024)
19-41687012-G-A		not specified	Uncertain significance (May 01, 2024)
19-41687025-A-C		not specified	Uncertain significance (Dec 14, 2021)
19-41687045-C-T		not specified	Uncertain significance (Jul 19, 2023)
19-41687047-A-G		not specified	Uncertain significance (Nov 27, 2023)
19-41687077-C-A		not specified	Uncertain significance (Dec 11, 2023)
19-41687092-T-C		not specified	Uncertain significance (Nov 18, 2022)
19-41687126-C-T		not specified	Uncertain significance (Dec 03, 2024)
19-41687147-C-G		not specified	Uncertain significance (Nov 24, 2024)
19-41687150-C-A		not specified	Uncertain significance (Jan 09, 2024)
19-41687150-C-T		not specified	Uncertain significance (Jul 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEACAM7	protein_coding	protein_coding	ENST00000006724	4	33661

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.35e-7	0.216	125138	1	602	125741	0.00240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.637	172	150	1.15	0.00000811	1711
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00129	0.00129
Ashkenazi Jewish	0.00663	0.00657
East Asian	0.000333	0.000326
Finnish	0.000370	0.000370
European (Non-Finnish)	0.00352	0.00346
Middle Eastern	0.000333	0.000326
South Asian	0.00271	0.00268
Other	0.00232	0.00228

dbNSFP

Source: dbNSFP

• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Intolerance Scores

• loftool: 0.849
• rvis_EVS: 0.97
• rvis_percentile_EVS: 90.34

Haploinsufficiency Scores

• pHI: 0.151
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0997

Gene Damage Prediction

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

Gene ontology

• Cellular component: extracellular region;plasma membrane;apical plasma membrane;anchored component of membrane