GeneBe

CLDN15

claudin 15, the group of Claudins

Basic information

Region (hg38): 7:101232092-101238820

Links

ENSG00000106404 ∙ NCBI:24146 ∙ OMIM:615778 ∙ HGNC:2036 ∙ Uniprot:P56746 ∙ 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 CLDN15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN15 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
16
clinvar
 16
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 16 0 0

Variants in CLDN15

This is a list of pathogenic ClinVar variants found in the CLDN15 region.

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

Position Type Phenotype Significance ClinVar
7-101232456-T-C not specified Uncertain significance (Feb 15, 2023)2484630
7-101232460-G-C not specified Uncertain significance (Oct 04, 2022)3145469
7-101232472-C-T not specified Uncertain significance (Aug 27, 2024)3493368
7-101232620-C-T not specified Uncertain significance (Nov 30, 2022)2351411
7-101232656-G-A not specified Uncertain significance (Jun 21, 2023)2589768
7-101232686-T-C not specified Uncertain significance (Aug 04, 2024)3493369
7-101232836-G-A not specified Uncertain significance (Feb 26, 2025)3833812
7-101232897-C-T not specified Uncertain significance (Apr 30, 2024)3267590
7-101232911-A-G not specified Uncertain significance (Feb 20, 2025)3833813
7-101234302-C-A not specified Uncertain significance (Jul 10, 2024)3493367
7-101234316-T-C not specified Uncertain significance (Oct 22, 2021)2256445
7-101234346-A-G not specified Uncertain significance (Nov 10, 2024)2228079
7-101234389-G-A not specified Uncertain significance (Oct 26, 2022)2224896
7-101234401-G-T not specified Uncertain significance (Dec 21, 2022)2338891
7-101234407-C-T not specified Uncertain significance (Oct 13, 2023)3145467
7-101237403-T-C not specified Uncertain significance (May 06, 2022)2287709
7-101237434-A-C not specified Uncertain significance (May 01, 2024)3267592
7-101237577-G-A not specified Uncertain significance (Apr 23, 2024)3267591

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CLDN15protein_codingprotein_codingENST00000401528 56729
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.02330.919125729061257350.0000239
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6661151370.8400.000007851433
Missense in Polyphen2049.5850.40335516
Synonymous-0.2236663.71.040.00000423479
Loss of Function1.6349.370.4274.85e-792

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002910.0000291
Ashkenazi Jewish0.000.00
East Asian0.00005480.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.00002690.0000264
Middle Eastern0.00005480.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Claudins function as major constituents of the tight junction complexes that regulate the permeability of epithelia. While some claudin family members function as impermeable barriers, others mediate the permeability to ions and small molecules. Often, several claudin family members are coexpressed and interact with each other, and this determines the overall permeability. CLDN15 forms tight junctions that mediate the paracellular transport of small monovalent cations along a concentration gradient, due to selective permeability for Na(+), Li(+) and K(+) ions, but selects against Cl(-) ions. Plays an important role in paracellular Na(+) transport in the intestine and in Na(+) homeostasis. Required for normal Na(+)-dependent intestinal nutrient uptake. {ECO:0000269|PubMed:12055082, ECO:0000269|PubMed:13129853}.;
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
0.140

Intolerance Scores

loftool
0.103
rvis_EVS
-0.34
rvis_percentile_EVS
30.07

Haploinsufficiency Scores

pHI
0.114
hipred
N
hipred_score
0.474
ghis
0.561

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.245

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cldn15
Phenotype
digestive/alimentary phenotype; cellular phenotype; endocrine/exocrine gland phenotype;

Zebrafish Information Network

Gene name
cldn15a
Affected structure
intestinal bulb
Phenotype tag
abnormal
Phenotype quality
structure

Gene ontology

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