CLDN9

claudin 9, the group of Claudins

Basic information

Region (hg38): 16:3012923-3014505

Links

ENSG00000213937NCBI:9080OMIM:615799HGNC:2051Uniprot:O95484AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • hearing loss, autosomal recessive 116 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Deafness, autosomal recessive 116ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingAudiologic/Otolaryngologic31175426

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLDN9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN9 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
6
clinvar
1
clinvar
7
missense
1
clinvar
37
clinvar
38
nonsense
0
start loss
0
frameshift
0
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 2 37 6 1

Variants in CLDN9

This is a list of pathogenic ClinVar variants found in the CLDN9 region.

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

Position Type Phenotype Significance ClinVar
16-3013374-C-T Likely benign (May 01, 2024)3067290
16-3013375-G-A not specified Uncertain significance (Jun 09, 2022)2412430
16-3013382-A-G not specified Uncertain significance (Dec 28, 2022)2339780
16-3013385-T-C not specified Uncertain significance (Oct 08, 2024)3493465
16-3013395-G-A not specified Uncertain significance (Apr 18, 2023)2537593
16-3013429-G-A not specified Uncertain significance (Apr 22, 2024)3267632
16-3013447-CT-C Hearing loss, autosomal recessive 116 Pathogenic (Jul 22, 2024)984737
16-3013462-G-A not specified Uncertain significance (Oct 01, 2024)3493463
16-3013499-T-G not specified Uncertain significance (Jun 09, 2022)2294964
16-3013520-C-A CLDN9-related disorder Likely benign (Jun 26, 2024)3354242
16-3013539-G-A Likely benign (Mar 01, 2023)2646094
16-3013558-G-C not specified Uncertain significance (Jan 02, 2024)3145532
16-3013561-T-C not specified Uncertain significance (Dec 06, 2022)2333680
16-3013584-G-A Benign (Nov 01, 2024)2498646
16-3013597-G-A not specified Uncertain significance (Oct 07, 2024)3493460
16-3013603-C-T Uncertain significance (May 01, 2023)2570928
16-3013624-C-G not specified Uncertain significance (Sep 20, 2024)3493461
16-3013670-A-G not specified Uncertain significance (Feb 23, 2023)2488444
16-3013680-G-A Likely benign (Dec 01, 2023)3024792
16-3013681-T-C not specified Uncertain significance (Aug 19, 2024)3493459
16-3013682-G-T not specified Uncertain significance (Apr 22, 2024)3267630
16-3013692-C-G CLDN9-related disorder • not specified Uncertain significance (Mar 29, 2023)2522829
16-3013697-G-A not specified Uncertain significance (Feb 23, 2023)2457387
16-3013705-G-A not specified Uncertain significance (May 31, 2022)2293219
16-3013708-C-T Hearing loss, autosomal recessive 116 Likely pathogenic (May 01, 2024)3250379

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CLDN9protein_codingprotein_codingENST00000445369 12050
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000006310.15600000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.081791431.260.000009281337
Missense in Polyphen8764.7781.343662
Synonymous-2.4210073.61.360.00000518522
Loss of Function-0.65475.371.302.33e-749

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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)

Intolerance Scores

loftool
0.146
rvis_EVS
-0.82
rvis_percentile_EVS
11.68

Haploinsufficiency Scores

pHI
0.208
hipred
N
hipred_score
0.339
ghis
0.643

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.286

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cldn9
Phenotype
hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process
calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules;cell-cell junction organization;viral entry into host cell
Cellular component
plasma membrane;bicellular tight junction;integral component of membrane;cell junction;intracellular membrane-bounded organelle
Molecular function
virus receptor activity;structural molecule activity;protein binding;identical protein binding