CLDN7

claudin 7, the group of Claudins

Basic information

Region (hg38): 17:7259903-7263983

Previous symbols: [ "CEPTRL2", "CPETRL2" ]

Links

ENSG00000181885 ∙ NCBI:1366 ∙ OMIM:609131 ∙ HGNC:2049 ∙ Uniprot:O95471 ∙ 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 CLDN7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN7 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				2		2
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	2	0

Variants in CLDN7

This is a list of pathogenic ClinVar variants found in the CLDN7 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7260415-G-A		not specified	Uncertain significance (Jan 27, 2022)
17-7260459-C-T		not specified	Uncertain significance (Jun 22, 2023)
17-7260487-C-G		not specified	Uncertain significance (Jun 13, 2023)
17-7260502-C-T		not specified	Uncertain significance (Nov 14, 2023)
17-7260515-G-A		not specified	Likely benign (Jun 05, 2023)
17-7260724-G-A		not specified	Uncertain significance (Feb 21, 2024)
17-7260724-G-C		not specified	Uncertain significance (Oct 03, 2023)
17-7260883-C-G		not specified	Uncertain significance (Jul 16, 2021)
17-7260892-C-A		not specified	Uncertain significance (May 04, 2022)
17-7260910-A-G		not specified	Uncertain significance (Feb 11, 2022)
17-7260912-C-T			Likely benign (Aug 09, 2018)
17-7260914-T-C		not specified	Uncertain significance (Sep 02, 2024)
17-7260941-G-C		not specified	Uncertain significance (Dec 10, 2024)
17-7260947-G-A		not specified	Likely benign (Oct 20, 2024)
17-7261961-G-A		not specified	Uncertain significance (Dec 19, 2022)
17-7262036-T-C		not specified	Uncertain significance (Jun 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLDN7	protein_coding	protein_coding	ENST00000360325	4	4081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00288	0.820	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.471	111	126	0.882	0.00000626	1354
Missense in Polyphen		33	38.837	0.8497		448
Synonymous	-0.373	54	50.6	1.07	0.00000258	434
Loss of Function	1.11	5	8.49	0.589	3.65e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.0000549	0.0000544
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. {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: 0.0868

Intolerance Scores

• loftool: 0.178
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.234
• hipred: N
• hipred_score: 0.490
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.344

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cldn7
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); renal/urinary system phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: cldn7a
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

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;basolateral plasma membrane
• Molecular function: structural molecule activity;protein binding;identical protein binding