CLDN22

claudin 22, the group of Claudins

Basic information

Region (hg38): 4:183318100-183320276

Links

ENSG00000177300 ∙ NCBI:53842 ∙ ∙ HGNC:2044 ∙ Uniprot:Q8N7P3 ∙ 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 CLDN22 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN22 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in CLDN22

This is a list of pathogenic ClinVar variants found in the CLDN22 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-183319563-T-A		not specified	Uncertain significance (Apr 04, 2024)
4-183319572-G-A		not specified	Uncertain significance (Feb 12, 2025)
4-183319617-A-G		not specified	Uncertain significance (Feb 14, 2023)
4-183319645-C-T		not specified	Uncertain significance (Jun 24, 2022)
4-183319651-T-C		not specified	Uncertain significance (Mar 14, 2023)
4-183319656-C-T		not specified	Uncertain significance (Jan 08, 2024)
4-183319669-G-T		not specified	Likely benign (Jun 17, 2024)
4-183319677-C-A		not specified	Uncertain significance (Dec 19, 2023)
4-183319683-C-T		not specified	Uncertain significance (Jun 23, 2023)
4-183319707-A-T		not specified	Uncertain significance (Nov 08, 2024)
4-183319734-A-G		not specified	Uncertain significance (Jan 08, 2024)
4-183319788-G-A		not specified	Uncertain significance (Oct 08, 2024)
4-183319810-C-T		not specified	Uncertain significance (Nov 22, 2022)
4-183319899-A-G		not specified	Likely benign (Dec 08, 2023)
4-183319912-C-T		not specified	Uncertain significance (Aug 20, 2024)
4-183319951-G-T		not specified	Uncertain significance (Dec 06, 2024)
4-183319967-C-T		not specified	Uncertain significance (Nov 29, 2023)
4-183319983-A-G		not specified	Uncertain significance (Jul 14, 2022)
4-183320019-A-G		not specified	Uncertain significance (Feb 14, 2025)
4-183320079-G-T		not specified	Uncertain significance (Jul 14, 2021)
4-183320083-A-G		not specified	Uncertain significance (Feb 07, 2023)
4-183320095-C-T		not specified	Uncertain significance (Jun 18, 2024)
4-183320149-A-G		not specified	Uncertain significance (Feb 23, 2023)
4-183320170-A-G		not specified	Uncertain significance (Sep 27, 2021)
4-183320182-C-T		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLDN22	protein_coding	protein_coding	ENST00000323319	1	2708

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0381	0.847	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.341	124	114	1.09	0.00000560	1402
Missense in Polyphen		46	37.447	1.2284		465
Synonymous	0.976	43	51.9	0.828	0.00000294	474
Loss of Function	1.27	3	6.49	0.462	3.61e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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: 0.0850

Intolerance Scores

• loftool: 0.561
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.11

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0817

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cldn22

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