CEACAM21

CEA cell adhesion molecule 21, the group of V-set domain containing|CEA cell adhesion molecule family

Basic information

Region (hg38): 19:41549517-41586844

Links

ENSG00000007129 ∙ NCBI:90273 ∙ OMIM:618191 ∙ HGNC:28834 ∙ Uniprot:Q3KPI0 ∙ 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 CEACAM21 gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEACAM21 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	11	1	0

Variants in CEACAM21

This is a list of pathogenic ClinVar variants found in the CEACAM21 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-41576281-C-A		not specified	Uncertain significance (Feb 21, 2024)
19-41576336-C-T		not specified	Likely benign (Jun 28, 2022)
19-41577200-C-T		not specified	Uncertain significance (Jul 27, 2022)
19-41577226-C-T		not specified	Uncertain significance (Dec 19, 2022)
19-41577340-A-C		not specified	Uncertain significance (Oct 06, 2022)
19-41577362-A-G		not specified	Uncertain significance (Mar 06, 2023)
19-41577397-G-A		not specified	Uncertain significance (Jan 22, 2024)
19-41577550-C-T		not specified	Uncertain significance (Nov 10, 2021)
19-41579440-C-T		not specified	Uncertain significance (Sep 22, 2022)
19-41579475-C-T		not specified	Uncertain significance (Apr 13, 2022)
19-41579479-T-G		not specified	Uncertain significance (Nov 14, 2023)
19-41579536-C-A		not specified	Uncertain significance (Oct 16, 2023)
19-41584358-A-G		not specified	Uncertain significance (Jan 04, 2022)
19-41584379-G-C		not specified	Uncertain significance (May 17, 2023)
19-41585450-G-A		not specified	Uncertain significance (Jun 28, 2022)
19-41585477-C-T		not specified	Uncertain significance (Nov 21, 2023)
19-41585480-C-A		not specified	Uncertain significance (Oct 12, 2022)
19-41585494-C-T			Likely benign (May 01, 2022)
19-41585852-C-T		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEACAM21	protein_coding	protein_coding	ENST00000401445	6	37312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.24e-12	0.0131	125667	0	8	125675	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.316	178	167	1.07	0.00000894	1884
Missense in Polyphen		46	37.436	1.2288		449
Synonymous	-0.543	73	67.3	1.08	0.00000397	593
Loss of Function	-0.530	17	14.8	1.15	7.82e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000138	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000364	0.0000352
Middle Eastern	0.000111	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.08
• rvis_percentile_EVS: 91.81

Haploinsufficiency Scores

• pHI: 0.0740
• hipred: N
• hipred_score: 0.182

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.315

Gene Damage Prediction

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

Gene ontology

• Cellular component: integral component of membrane