CLDN20

claudin 20, the group of Claudins

Basic information

Region (hg38): 6:155264013-155276548

Links

ENSG00000171217 ∙ NCBI:49861 ∙ ∙ HGNC:2042 ∙ Uniprot:P56880 ∙ 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 CLDN20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN20 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in CLDN20

This is a list of pathogenic ClinVar variants found in the CLDN20 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-155275834-A-G		not specified	Uncertain significance (Oct 25, 2022)
6-155275856-A-G		not specified	Uncertain significance (Nov 30, 2021)
6-155275864-G-A		not specified	Uncertain significance (Dec 19, 2022)
6-155275883-C-T		not specified	Uncertain significance (Dec 13, 2023)
6-155275958-C-T		not specified	Uncertain significance (Jan 23, 2023)
6-155276077-G-C		not specified	Uncertain significance (May 20, 2024)
6-155276123-C-T		not specified	Uncertain significance (Dec 03, 2021)
6-155276150-T-C		not specified	Uncertain significance (Oct 13, 2023)
6-155276174-T-C		not specified	Uncertain significance (Mar 06, 2023)
6-155276324-T-C		not specified	Uncertain significance (May 20, 2024)
6-155276351-C-A		not specified	Uncertain significance (Sep 13, 2023)
6-155276363-T-C		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLDN20	protein_coding	protein_coding	ENST00000367165	1	12536

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00489	0.471	124906	14	825	125745	0.00334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.152	126	121	1.04	0.00000610	1420
Missense in Polyphen		48	43.298	1.1086		514
Synonymous	0.783	42	49.0	0.858	0.00000279	467
Loss of Function	-0.251	3	2.57	1.17	1.07e-7	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.00109	0.00109
Finnish	0.0314	0.0313
European (Non-Finnish)	0.000968	0.000967
Middle Eastern	0.00109	0.00109
South Asian	0.000426	0.000392
Other	0.00424	0.00424

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium- independent cell-adhesion activity. {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: 0.109

Intolerance Scores

• loftool: 0.381
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.96

Haploinsufficiency Scores

• pHI: 0.0884
• hipred: N
• hipred_score: 0.190
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cldn20

Gene ontology

• Biological process: calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules
• Cellular component: plasma membrane;bicellular tight junction;integral component of membrane
• Molecular function: structural molecule activity;identical protein binding