CLDN25

claudin 25, the group of Claudins

Basic information

Region (hg38): 11:113779796-113780485

Links

ENSG00000228607 ∙ NCBI:644672 ∙ ∙ HGNC:37218 ∙ Uniprot:C9JDP6 ∙ 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 CLDN25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN25 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	1		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	15	1	0

Variants in CLDN25

This is a list of pathogenic ClinVar variants found in the CLDN25 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-113779847-C-T		not specified	Uncertain significance (Apr 26, 2024)
11-113779919-G-A		not specified	Uncertain significance (Jan 31, 2024)
11-113779973-G-A		not specified	Uncertain significance (May 24, 2024)
11-113780006-T-G		not specified	Uncertain significance (Nov 03, 2023)
11-113780042-C-T		not specified	Uncertain significance (Oct 05, 2023)
11-113780084-C-T		not specified	Uncertain significance (Jan 17, 2023)
11-113780144-C-T		not specified	Uncertain significance (May 08, 2023)
11-113780150-G-C		not specified	Uncertain significance (Jun 01, 2022)
11-113780157-T-C		not specified	Uncertain significance (Mar 07, 2024)
11-113780166-C-T		not specified	Uncertain significance (Mar 27, 2023)
11-113780211-G-C		not specified	Uncertain significance (Feb 27, 2024)
11-113780234-G-A		not specified	Uncertain significance (Mar 23, 2023)
11-113780239-C-G		not specified	Uncertain significance (Oct 03, 2022)
11-113780261-A-G		not specified	Uncertain significance (Jan 02, 2024)
11-113780417-T-C		not specified	Uncertain significance (Oct 26, 2022)
11-113780460-T-C		not specified	Likely benign (Nov 30, 2021)
11-113780466-C-T		not specified	Uncertain significance (Dec 09, 2023)
11-113780481-T-C		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLDN25	protein_coding	protein_coding	ENST00000453129	1	754

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.51e-8	0.0338	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.739	151	128	1.18	0.00000673	1473
Missense in Polyphen		45	32.715	1.3755		393
Synonymous	0.523	47	51.8	0.907	0.00000264	501
Loss of Function	-1.24	10	6.56	1.52	3.51e-7	58

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}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Tight junction - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.575
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cldn25-ps

Gene ontology

• Cellular component: plasma membrane;bicellular tight junction;integral component of membrane
• Molecular function: structural molecule activity