CLDN20

protein-coding

claudin 20, the group of Claudins

Gene summary

This gene encodes a member of the claudin family. Claudins are integral membrane proteins and components of tight junction strands. Tight junction strands serve as a physical barrier to prevent solutes and water from passing freely through the paracellular space between epithelial or endothelial cell sheets, and also play critical roles in maintaining cell polarity and signal transductions. [provided by RefSeq, Jun 2010]

MANE transcript

NM_001001346.3

Inheritance

—

ClinVar variants

U:30B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.17

Max pathogenic AF

—

Genomic locus

chr6:155,264,013-155,276,548

External References & Databases

Ensembl (ENSG00000171217)

Transcript & Mutation Effects

hg38 • Region Span ~12.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CLDN20 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 28

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001001346.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			29 clinvar		1 clinvar	30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	0	1	31

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001001346.3	RefSeq	NP_001001346.1	1	MANE Select
ENST00000367165.3	Ensembl	ENSP00000356133.3	1	MANE Select
ENST00000909656.1	Ensembl	ENSP00000579715.1	1	Standard
ENST00000909656.2	Ensembl	ENSP00000579715.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules

Molecular Function

structural molecule activity
identical protein binding

Cellular Component

plasma membrane
bicellular tight junction
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367165
Coding exons: 1
Length: 12536
Individuals with no LoFs: 124906
Homozygous LoFs: 14
Heterozygous LoFs: 825
Defined: 125745
p: 0.00334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.152	126	121	1.04	0.00000610	1420
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0011	0.0011	notable
Finnish	0.031	0.031	notable
European (Non-Finnish)	0.00097	0.00097	rare
South Asian	0.00043	0.00039	rare
Other	0.0042	0.0042	notable

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.381
RVIS EVS: 0.42
RVIS percentile EVS: 76.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.200

Gene Damage Prediction

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