CLDN3

claudin 3, the group of Claudins

Basic information

Region (hg38): 7:73768997-73770270

Previous symbols: [ "C7orf1", "CPETR2" ]

Links

ENSG00000165215

∙ NCBI:1365 ∙ OMIM:602910 ∙ HGNC:2045 ∙ Uniprot:O15551 ∙ 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 CLDN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN3 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			15 clinvar			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in CLDN3

This is a list of pathogenic ClinVar variants found in the CLDN3 region.

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

Position	Phenotype	Significance	ClinVar
7-73769403-C-A	not specified	Uncertain significance (Mar 25, 2024)	3267619
7-73769416-T-A	not specified	Uncertain significance (Feb 07, 2025)	3833852
7-73769475-G-T	not specified	Uncertain significance (Nov 06, 2024)	3493426
7-73769487-T-C	not specified	Uncertain significance (Aug 19, 2024)	3493421
7-73769490-C-T	not specified	Uncertain significance (Dec 17, 2023)	3145513
7-73769494-G-A	not specified	Uncertain significance (Dec 31, 2024)	3833851
7-73769517-G-A	not specified	Uncertain significance (Feb 07, 2025)	3833850
7-73769557-C-A	not specified	Uncertain significance (Aug 28, 2024)	3493424
7-73769593-C-T	not specified	Uncertain significance (Mar 04, 2024)	3145511
7-73769635-C-T	not specified	Uncertain significance (Oct 19, 2024)	3493420
7-73769662-G-A	not specified	Uncertain significance (Jan 03, 2024)	3145510
7-73769761-C-A	not specified	Uncertain significance (Mar 07, 2024)	3145509
7-73769800-C-G	not specified	Uncertain significance (May 20, 2024)	2402976
7-73769827-C-G	not specified	Uncertain significance (Aug 28, 2024)	3493422
7-73769944-C-T	not specified	Uncertain significance (Jun 12, 2023)	2559763
7-73769966-C-T	not specified	Uncertain significance (Oct 24, 2024)	3493425
7-73769986-C-A	not specified	Uncertain significance (Mar 01, 2025)	3833853
7-73769986-C-T	not specified	Uncertain significance (Apr 19, 2024)	3267620
7-73770046-A-T	not specified	Uncertain significance (Feb 26, 2024)	3145512

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLDN3	protein_coding	protein_coding	ENST00000395145	1	1273

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.522	0.463	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	106	152	0.697	0.00000997	1375
Missense in Polyphen		25	55.875	0.44743		584
Synonymous	1.15	69	82.2	0.839	0.00000621	506
Loss of Function	1.95	1	6.28	0.159	2.74e-7	52

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|UniProtKB:Q9Z0G9}.;
Disease: DISEASE: Note=CLDN3 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region.;
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: 0.111

Intolerance Scores

loftool
rvis_EVS: 0.42
rvis_percentile_EVS: 76.81

Haploinsufficiency Scores

pHI: 0.196
hipred: N
hipred_score: 0.481
ghis: 0.553

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.694

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cldn3
Phenotype

Gene ontology

Biological process: response to hypoxia;epithelial cell morphogenesis;calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules;response to ethanol;protein homooligomerization;protein heterooligomerization;bicellular tight junction assembly
Cellular component: cytoplasm;integral component of plasma membrane;bicellular tight junction;integral component of membrane;apicolateral plasma membrane;lateral plasma membrane
Molecular function: transmembrane signaling receptor activity;structural molecule activity;identical protein binding