CLDN18

claudin 18, the group of Claudins

Basic information

Region (hg38): 3:137998735-138033655

Previous symbols: [ "SFTPJ" ]

Links

ENSG00000066405 ∙ NCBI:51208 ∙ OMIM:609210 ∙ HGNC:2039 ∙ Uniprot:P56856 ∙ 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 CLDN18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN18 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 CLDN18

This is a list of pathogenic ClinVar variants found in the CLDN18 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-137998975-A-C		not specified	Uncertain significance (Aug 12, 2021)
3-138010238-A-T		not specified	Uncertain significance (Feb 27, 2025)
3-138010393-G-C		not specified	Uncertain significance (Feb 15, 2023)
3-138023670-C-T		not specified	Uncertain significance (Oct 08, 2024)
3-138023679-C-T		not specified	Uncertain significance (Apr 25, 2023)
3-138023711-A-G		not specified	Uncertain significance (Dec 11, 2024)
3-138023712-T-C		not specified	Uncertain significance (May 26, 2023)
3-138023750-C-T		not specified	Uncertain significance (Jan 09, 2025)
3-138023814-T-C		not specified	Uncertain significance (Oct 17, 2024)
3-138024690-G-A		not specified	Uncertain significance (Jun 13, 2022)
3-138024697-G-A		not specified	Uncertain significance (Jun 11, 2021)
3-138029810-G-A		not specified	Uncertain significance (Dec 21, 2023)
3-138029810-G-T		not specified	Likely benign (Jan 31, 2024)
3-138029834-G-A		not specified	Uncertain significance (Nov 18, 2024)
3-138029868-T-A		not specified	Uncertain significance (Apr 04, 2024)
3-138029870-T-A		not specified	Uncertain significance (Jan 03, 2024)
3-138029877-C-T		not specified	Uncertain significance (Dec 28, 2023)
3-138029883-G-A		not specified	Uncertain significance (Mar 16, 2022)
3-138030989-C-G		not specified	Uncertain significance (Mar 07, 2023)
3-138031043-G-A		not specified	Uncertain significance (Dec 14, 2021)
3-138031083-G-A		not specified	Uncertain significance (Feb 09, 2025)
3-138031103-G-A		not specified	Uncertain significance (Dec 19, 2023)
3-138031125-A-G		not specified	Uncertain significance (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLDN18	protein_coding	protein_coding	ENST00000183605	5	34918

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000187	0.725	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.607	135	156	0.863	0.00000867	1681
Missense in Polyphen		43	53.533	0.80324		590
Synonymous	0.414	61	65.3	0.935	0.00000439	533
Loss of Function	0.956	7	10.3	0.679	5.25e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000905	0.000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000231	0.000231
European (Non-Finnish)	0.0000535	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.000196	0.000196
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);EMT transition in Colorectal Cancer;Tight junction interactions;Cell-cell junction organization;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.209
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.8

Haploinsufficiency Scores

• pHI: 0.148
• hipred: N
• hipred_score: 0.292

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.210

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cldn18
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; skeleton phenotype; immune system phenotype; digestive/alimentary phenotype; hematopoietic system phenotype; respiratory system phenotype

Gene ontology

• Biological process: calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules;response to ethanol;negative regulation of bone resorption;digestive tract development;TNFSF11-mediated signaling pathway;negative regulation of protein localization to nucleus;negative regulation of osteoclast development
• Cellular component: plasma membrane;bicellular tight junction;integral component of membrane
• Molecular function: structural molecule activity;identical protein binding