CGN

cingulin

Basic information

Region (hg38): 1:151510510-151538692

Links

ENSG00000143375 ∙ NCBI:57530 ∙ OMIM:609473 ∙ HGNC:17429 ∙ Uniprot:Q9P2M7 ∙ 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 CGN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CGN 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				1	1	2
missense			79	7	3	89
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	79	8	4

Variants in CGN

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

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

Position	Type	Phenotype	Significance	ClinVar
1-151518550-C-T			Likely benign (Mar 01, 2023)
1-151518589-A-G		not specified	Uncertain significance (Feb 12, 2024)
1-151518590-C-T		not specified	Uncertain significance (Aug 30, 2022)
1-151518619-A-G		not specified	Uncertain significance (Dec 22, 2023)
1-151518623-T-C		not specified	Uncertain significance (Jun 21, 2021)
1-151518635-G-A		not specified	Uncertain significance (May 11, 2022)
1-151518699-C-T			Benign (Apr 04, 2018)
1-151518700-G-T		not specified	Uncertain significance (Apr 07, 2022)
1-151518765-C-G		not specified	Uncertain significance (May 03, 2023)
1-151518803-G-A		not specified	Uncertain significance (Mar 16, 2022)
1-151518899-A-C		not specified	Uncertain significance (May 07, 2024)
1-151518944-C-T		not specified	Uncertain significance (Jan 04, 2022)
1-151518965-C-A		not specified	Uncertain significance (Dec 02, 2022)
1-151518997-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-151518998-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-151519001-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-151519049-C-T		not specified	Uncertain significance (Sep 29, 2022)
1-151519114-C-T		not specified	Uncertain significance (Jun 23, 2023)
1-151519115-G-A		not specified	Uncertain significance (Oct 10, 2023)
1-151519172-G-A		not specified	Uncertain significance (Jan 06, 2023)
1-151519181-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-151519189-T-G		not specified	Uncertain significance (Apr 22, 2024)
1-151519198-C-T			Likely benign (Mar 28, 2018)
1-151519249-C-G		not specified	Uncertain significance (Aug 22, 2023)
1-151519349-T-C		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CGN	protein_coding	protein_coding	ENST00000271636	20	28183

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.89e-31	0.0500	125475	0	273	125748	0.00109

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.170	695	708	0.982	0.0000460	7704
Missense in Polyphen		262	268.16	0.97702		2851
Synonymous	1.50	243	275	0.885	0.0000143	2479
Loss of Function	1.93	58	76.2	0.762	0.00000523	711

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00216	0.00216
Ashkenazi Jewish	0.00228	0.00228
East Asian	0.00127	0.00125
Finnish	0.000972	0.000971
European (Non-Finnish)	0.00119	0.00118
Middle Eastern	0.00127	0.00125
South Asian	0.000558	0.000555
Other	0.00163	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably plays a role in the formation and regulation of the tight junction (TJ) paracellular permeability barrier.
• Pathway: Tight junction - Homo sapiens (human);Signal Transduction;TCR;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) (Consensus)

Recessive Scores

• pRec: 0.405

Intolerance Scores

• loftool: 0.782
• rvis_EVS: 1.97
• rvis_percentile_EVS: 97.57

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.492
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.511

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cgn
• Phenotype: homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype

Gene ontology

• Biological process: transforming growth factor beta receptor signaling pathway;biological_process
• Cellular component: plasma membrane;bicellular tight junction;myosin complex;cell junction
• Molecular function: motor activity;actin binding;protein binding;cadherin binding