CLDN12

claudin 12, the group of Claudins

Basic information

Region (hg38): 7:90383721-90513402

Links

ENSG00000157224 ∙ NCBI:9069 ∙ OMIM:611232 ∙ HGNC:2034 ∙ Uniprot:P56749 ∙ 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 CLDN12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN12 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in CLDN12

This is a list of pathogenic ClinVar variants found in the CLDN12 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-90384910-A-C		not specified	Uncertain significance (Aug 02, 2022)
7-90384944-C-G		not specified	Uncertain significance (May 03, 2023)
7-90384958-C-T		not specified	Uncertain significance (Nov 21, 2022)
7-90384970-T-A		not specified	Uncertain significance (Nov 13, 2024)
7-90385005-A-G		not specified	Uncertain significance (Feb 10, 2025)
7-90385017-C-G		not specified	Uncertain significance (Aug 01, 2024)
7-90385035-C-G		not specified	Uncertain significance (Feb 16, 2023)
7-90412686-C-T		not specified	Uncertain significance (Dec 21, 2022)
7-90412698-G-A		not specified	Uncertain significance (Nov 21, 2024)
7-90412725-G-A		not specified	Uncertain significance (Jul 26, 2022)
7-90413041-T-A		not specified	Uncertain significance (Oct 18, 2021)
7-90413211-A-G		not specified	Uncertain significance (Aug 21, 2023)
7-90413289-C-T		not specified	Uncertain significance (Nov 24, 2024)
7-90413297-G-T		not specified	Uncertain significance (Jan 20, 2025)
7-90413403-A-G		not specified	Uncertain significance (Jan 23, 2024)
7-90469843-T-C			Likely benign (Oct 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLDN12	protein_coding	protein_coding	ENST00000535571	1	129682

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0485	0.866	125716	0	6	125722	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	97	134	0.723	0.00000734	1566
Missense in Polyphen		37	50.624	0.73088		571
Synonymous	-1.25	67	55.2	1.21	0.00000287	534
Loss of Function	1.42	3	7.07	0.424	4.04e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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: EMT transition in Colorectal Cancer;Tight junction interactions;Cell-cell junction organization;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.548
• hipred: N
• hipred_score: 0.459
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.868

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cldn12

Gene ontology

• Biological process: calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules
• Cellular component: plasma membrane;bicellular tight junction;integral component of membrane;lateral plasma membrane
• Molecular function: structural molecule activity;protein binding;identical protein binding