CLDN11

claudin 11, the group of MicroRNA protein coding host genes|Claudins

Basic information

Region (hg38): 3:170418868-170454733

Previous symbols: [ "OTM" ]

Links

ENSG00000013297 ∙ NCBI:5010 ∙ OMIM:601326 ∙ HGNC:8514 ∙ Uniprot:O75508 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• leukodystrophy, hypomyelinating, 22 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Leukodystrophy, hypomyelinating, 22	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	Neurologic; Ophthalmologic	33313762

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLDN11 gene.

• Leukodystrophy, hypomyelinating, 22 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN11 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				3	1	4
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	3	1

Variants in CLDN11

This is a list of pathogenic ClinVar variants found in the CLDN11 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-170419158-TGGTGACCTGCGG-T		Marfanoid habitus and intellectual disability	Uncertain significance (-)
3-170419219-G-T			Likely benign (Dec 01, 2022)
3-170419245-C-G		Leukodystrophy, hypomyelinating, 22	Uncertain significance (Mar 26, 2024)
3-170423168-G-A		Leukodystrophy, hypomyelinating, 22	Uncertain significance (Dec 30, 2023)
3-170423272-C-T			Likely benign (Feb 01, 2022)
3-170432640-G-A		not specified	Uncertain significance (Feb 27, 2023)
3-170432640-G-C		not specified	Uncertain significance (Feb 15, 2023)
3-170432695-A-G		not specified	Uncertain significance (Nov 07, 2022)
3-170432733-C-T			Uncertain significance (Feb 01, 2023)
3-170432738-G-A			Benign (Apr 01, 2024)
3-170432747-C-G			Likely benign (Sep 01, 2023)
3-170432754-T-C		Leukodystrophy, hypomyelinating, 22	Pathogenic (Jul 23, 2021)
3-170432754-T-G		Leukodystrophy, hypomyelinating, 22	Pathogenic (May 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLDN11	protein_coding	protein_coding	ENST00000064724	3	441517

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.911	0.0886	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	72	128	0.562	0.00000800	1296
Missense in Polyphen		28	58.096	0.48196		600
Synonymous	0.884	50	58.6	0.853	0.00000399	463
Loss of Function	2.58	0	7.78	0.00	3.36e-7	77

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);Ectoderm Differentiation;EMT transition in Colorectal Cancer;Tight junction interactions;Cell-cell junction organization;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.269

Intolerance Scores

• loftool: 0.115
• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• pHI: 0.178
• hipred: Y
• hipred_score: 0.530
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.507

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cldn11
• Phenotype: endocrine/exocrine gland phenotype; cellular 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype

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
• Molecular function: structural molecule activity;protein binding;identical protein binding