CLDN9
Basic information
Region (hg38): 16:3012923-3014505
Links
Phenotypes
GenCC
Source:
- hearing loss, autosomal recessive 116 (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Deafness, autosomal recessive 116 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Audiologic/Otolaryngologic | 31175426 |
ClinVar
This is a list of variants' phenotypes submitted to
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 | 7 | |||||
missense | 37 | 38 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 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) | |||
16-3013375-G-A | not specified | Uncertain significance (Jun 09, 2022) | ||
16-3013382-A-G | not specified | Uncertain significance (Dec 28, 2022) | ||
16-3013385-T-C | not specified | Uncertain significance (Oct 08, 2024) | ||
16-3013395-G-A | not specified | Uncertain significance (Apr 18, 2023) | ||
16-3013429-G-A | not specified | Uncertain significance (Apr 22, 2024) | ||
16-3013447-CT-C | Hearing loss, autosomal recessive 116 | Pathogenic (Jul 22, 2024) | ||
16-3013462-G-A | not specified | Uncertain significance (Oct 01, 2024) | ||
16-3013499-T-G | not specified | Uncertain significance (Jun 09, 2022) | ||
16-3013520-C-A | CLDN9-related disorder | Likely benign (Jun 26, 2024) | ||
16-3013539-G-A | Likely benign (Mar 01, 2023) | |||
16-3013558-G-C | not specified | Uncertain significance (Jan 02, 2024) | ||
16-3013561-T-C | not specified | Uncertain significance (Dec 06, 2022) | ||
16-3013584-G-A | Benign (Nov 01, 2024) | |||
16-3013597-G-A | not specified | Uncertain significance (Oct 07, 2024) | ||
16-3013603-C-T | Uncertain significance (May 01, 2023) | |||
16-3013624-C-G | not specified | Uncertain significance (Sep 20, 2024) | ||
16-3013670-A-G | not specified | Uncertain significance (Feb 23, 2023) | ||
16-3013680-G-A | Likely benign (Dec 01, 2023) | |||
16-3013681-T-C | not specified | Uncertain significance (Aug 19, 2024) | ||
16-3013682-G-T | not specified | Uncertain significance (Apr 22, 2024) | ||
16-3013692-C-G | CLDN9-related disorder • not specified | Uncertain significance (Mar 29, 2023) | ||
16-3013697-G-A | not specified | Uncertain significance (Feb 23, 2023) | ||
16-3013705-G-A | not specified | Uncertain significance (May 31, 2022) | ||
16-3013708-C-T | Hearing loss, autosomal recessive 116 | Likely pathogenic (May 01, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CLDN9 | protein_coding | protein_coding | ENST00000445369 | 1 | 2050 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000631 | 0.156 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -1.08 | 179 | 143 | 1.26 | 0.00000928 | 1337 |
Missense in Polyphen | 87 | 64.778 | 1.343 | 662 | ||
Synonymous | -2.42 | 100 | 73.6 | 1.36 | 0.00000518 | 522 |
Loss of Function | -0.654 | 7 | 5.37 | 1.30 | 2.33e-7 | 49 |
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:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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