CGNL1

cingulin like 1

Basic information

Region (hg38): 15:57375966-57550717

Links

ENSG00000128849 ∙ NCBI:84952 ∙ OMIM:607856 ∙ HGNC:25931 ∙ Uniprot:Q0VF96 ∙ 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 CGNL1 gene.

• Inborn genetic diseases (91 variants)
• not provided (7 variants)
• CGNL1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CGNL1 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				2	2	4
missense			90	4		94
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	90	6	3

Variants in CGNL1

This is a list of pathogenic ClinVar variants found in the CGNL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-57438044-T-C		CGNL1-related disorder	Likely benign (Jan 27, 2020)
15-57438096-C-A		not specified	Uncertain significance (Dec 03, 2021)
15-57438110-A-G		CGNL1-related disorder	Likely benign (Apr 19, 2019)
15-57438120-G-C		not specified	Uncertain significance (Apr 07, 2023)
15-57438184-G-C		not specified	Uncertain significance (Nov 22, 2022)
15-57438189-C-G		not specified	Uncertain significance (Feb 06, 2024)
15-57438202-C-G		not specified	Uncertain significance (Jul 25, 2023)
15-57438232-C-A		not specified	Uncertain significance (Dec 21, 2023)
15-57438293-T-G		not specified	Uncertain significance (May 24, 2023)
15-57438318-C-G		not specified	Uncertain significance (Jan 23, 2024)
15-57438334-G-A		not specified	Uncertain significance (Apr 25, 2022)
15-57438339-A-G		not specified	Likely benign (Aug 13, 2021)
15-57438393-C-G		not specified	Uncertain significance (Feb 08, 2023)
15-57438420-C-T		not specified	Uncertain significance (Feb 28, 2024)
15-57438444-C-T		not specified	Uncertain significance (Feb 05, 2024)
15-57438459-C-A		CGNL1-related disorder	Uncertain significance (Feb 05, 2024)
15-57438504-C-G		not specified	Uncertain significance (Dec 08, 2021)
15-57438505-C-T		not specified	Uncertain significance (Jul 26, 2021)
15-57438624-G-A		not specified	Uncertain significance (Nov 17, 2022)
15-57438637-T-C		not specified	Uncertain significance (Sep 17, 2021)
15-57438673-A-T		not specified	Uncertain significance (Jan 27, 2022)
15-57438700-G-A		not specified	Uncertain significance (Jan 04, 2022)
15-57438715-G-C		not specified	Uncertain significance (Aug 17, 2021)
15-57438795-C-G		not specified	Uncertain significance (Feb 28, 2024)
15-57438796-C-T		not specified	Uncertain significance (Jul 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CGNL1	protein_coding	protein_coding	ENST00000281282	18	174761

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.69e-42	7.59e-7	125541	1	206	125748	0.000823

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.02	881	728	1.21	0.0000442	8553
Missense in Polyphen		242	211.99	1.1416		2541
Synonymous	-0.870	320	301	1.06	0.0000189	2468
Loss of Function	-0.0509	63	62.6	1.01	0.00000349	748

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00304	0.00302
Ashkenazi Jewish	0.000303	0.000298
East Asian	0.000925	0.000925
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000416	0.000413
Middle Eastern	0.000925	0.000925
South Asian	0.000852	0.000850
Other	0.00261	0.00261

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in anchoring the apical junctional complex, especially tight junctions, to actin-based cytoskeletons. {ECO:0000269|PubMed:22891260}.
• Disease: DISEASE: Aromatase excess syndrome (AEXS) [MIM:139300]: An autosomal dominant disorder characterized by increased extraglandular aromatization of steroids that presents with heterosexual precocity in males and isosexual precocity in females. {ECO:0000269|PubMed:12736278}. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration inv(15)(q21.2;q21.3) has been found in patients with aromatase excess syndrome. The inversion moves the promoter of the CGNL1 gene into a 5-prime position in relation to the aromatase coding region.
• Pathway: Tight junction - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.903
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.43

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.329
• ghis: 0.488

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.735

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cgnl1

Gene ontology

• Biological process: actin filament organization;negative regulation of small GTPase mediated signal transduction
• Cellular component: bicellular tight junction;myosin complex
• Molecular function: motor activity;protein binding