CLDN6

claudin 6, the group of Claudins

Basic information

Region (hg38): 16:3014711-3020071

Links

ENSG00000184697 ∙ NCBI:9074 ∙ OMIM:615798 ∙ HGNC:2048 ∙ Uniprot:P56747 ∙ 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 CLDN6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN6 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
missense			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	1

Variants in CLDN6

This is a list of pathogenic ClinVar variants found in the CLDN6 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-3015390-G-A		not specified	Uncertain significance (Apr 03, 2023)
16-3015408-G-A		not specified	Uncertain significance (Oct 12, 2022)
16-3015431-C-T		not specified	Uncertain significance (Oct 25, 2023)
16-3015516-G-A		not specified	Uncertain significance (Nov 10, 2022)
16-3015538-C-A		not specified	Uncertain significance (Dec 01, 2022)
16-3015579-T-C		not specified	Uncertain significance (Mar 02, 2023)
16-3015588-C-T		not specified	Likely benign (Feb 10, 2022)
16-3015616-C-T		not specified	Uncertain significance (Apr 16, 2024)
16-3015618-G-C		not specified	Uncertain significance (Nov 12, 2021)
16-3015643-T-C		not specified	Uncertain significance (Oct 20, 2023)
16-3015676-G-A		not specified	Uncertain significance (Dec 21, 2022)
16-3015696-T-C		not specified	Uncertain significance (Feb 16, 2023)
16-3015763-C-T		not specified	Likely benign (Jun 18, 2021)
16-3015781-G-A		not specified	Uncertain significance (Jun 17, 2024)
16-3015807-G-A		not specified	Uncertain significance (Mar 01, 2023)
16-3015901-C-A		not specified	Uncertain significance (Jun 01, 2023)
16-3015980-T-C			Benign (Jun 04, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLDN6	protein_coding	protein_coding	ENST00000396925	1	5360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00404	0.668	125697	0	11	125708	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.428	148	134	1.10	0.00000844	1365
Missense in Polyphen		59	54.636	1.0799		614
Synonymous	-2.18	85	63.0	1.35	0.00000416	509
Loss of Function	0.602	4	5.53	0.724	2.40e-7	60

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000621	0.0000616
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a major role in tight junction-specific obliteration of the intercellular space. {ECO:0000250}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Tight junction - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);EMT transition in Colorectal Cancer;Tight junction interactions;Cell-cell junction organization;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.204
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.524
• hipred: N
• hipred_score: 0.386
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.910

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cldn6
• Phenotype: limbs/digits/tail phenotype; pigmentation phenotype; normal phenotype; 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; craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules;cell-cell junction organization;viral entry into host cell
• Cellular component: plasma membrane;bicellular tight junction;integral component of membrane;apicolateral plasma membrane
• Molecular function: virus receptor activity;structural molecule activity;protein binding;identical protein binding