CLDN17

claudin 17, the group of Claudins

Basic information

Region (hg38): 21:30165565-30166805

Links

ENSG00000156282 ∙ NCBI:26285 ∙ OMIM:617005 ∙ HGNC:2038 ∙ Uniprot:P56750 ∙ 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 CLDN17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN17 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in CLDN17

This is a list of pathogenic ClinVar variants found in the CLDN17 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-30166076-A-C		not specified	Uncertain significance (Feb 07, 2023)
21-30166098-C-G		not specified	Uncertain significance (Apr 22, 2022)
21-30166152-C-T		not specified	Uncertain significance (Apr 01, 2024)
21-30166232-G-A		not specified	Uncertain significance (Dec 19, 2023)
21-30166275-T-C		not specified	Uncertain significance (Jun 11, 2024)
21-30166277-G-A		not specified	Likely benign (Dec 11, 2024)
21-30166355-A-G		not specified	Uncertain significance (Oct 20, 2023)
21-30166368-T-C		not specified	Uncertain significance (Apr 06, 2023)
21-30166380-C-G		not specified	Uncertain significance (Feb 13, 2023)
21-30166383-T-C		not specified	Likely benign (Aug 01, 2022)
21-30166397-G-A		not specified	Uncertain significance (Oct 01, 2024)
21-30166400-A-C		not specified	Uncertain significance (Jul 14, 2022)
21-30166415-C-T		not specified	Uncertain significance (Jan 03, 2024)
21-30166432-C-A		not specified	Uncertain significance (Jan 18, 2022)
21-30166445-G-T		not specified	Uncertain significance (Dec 09, 2024)
21-30166493-A-G		not specified	Uncertain significance (Jun 11, 2021)
21-30166496-A-T		not specified	Uncertain significance (Oct 12, 2022)
21-30166523-A-T		not specified	Uncertain significance (Jun 16, 2023)
21-30166547-G-T		not specified	Uncertain significance (May 03, 2023)
21-30166565-A-C		not specified	Uncertain significance (Oct 17, 2023)
21-30166584-C-G		not specified	Uncertain significance (Mar 14, 2025)
21-30166604-G-T		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLDN17	protein_coding	protein_coding	ENST00000286808	1	731

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000334	0.384	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.256	137	129	1.06	0.00000695	1432
Missense in Polyphen		47	45.808	1.026		541
Synonymous	-1.03	61	51.6	1.18	0.00000286	491
Loss of Function	-0.104	5	4.76	1.05	2.89e-7	45

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: Channel-forming tight junction protein with selectivity for anions, including chloride and bicarbonate, and for solutes smaller than 9 Angstrom in diameter. In the kidney proximal tubule, may be involved in quantitative reabsorption of filtered anions. Does not affect water permeability. {ECO:0000269|PubMed:22402829}.
• 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: 0.101

Intolerance Scores

• loftool: 0.399
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.0428
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0958

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cldn17

Gene ontology

• Biological process: calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules;chloride transmembrane transport
• Cellular component: plasma membrane;bicellular tight junction;chloride channel complex
• Molecular function: structural molecule activity;chloride channel activity;protein binding;identical protein binding