CLDND1

claudin domain containing 1

Basic information

Region (hg38): 3:98497911-98523066

Previous symbols: [ "C3orf4" ]

Links

ENSG00000080822 ∙ NCBI:56650 ∙ OMIM:619677 ∙ HGNC:1322 ∙ Uniprot:Q9NY35 ∙ 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 CLDND1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDND1 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in CLDND1

This is a list of pathogenic ClinVar variants found in the CLDND1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-98497921-A-T		not specified	Uncertain significance (Nov 08, 2022)
3-98498027-C-T		not specified	Uncertain significance (Nov 30, 2021)
3-98498075-A-G		not specified	Uncertain significance (Oct 10, 2023)
3-98498156-A-G		not specified	Uncertain significance (Oct 17, 2023)
3-98498192-T-C		not specified	Likely benign (Oct 17, 2023)
3-98498215-T-C		not specified	Uncertain significance (Mar 31, 2024)
3-98498234-A-G		not specified	Uncertain significance (Jun 10, 2024)
3-98498254-C-T		not specified	Uncertain significance (Mar 24, 2023)
3-98498270-T-C		not specified	Uncertain significance (Dec 14, 2023)
3-98498329-T-A		not specified	Uncertain significance (Oct 20, 2023)
3-98498383-G-A		not specified	Uncertain significance (Apr 19, 2023)
3-98498407-T-A		not specified	Uncertain significance (May 10, 2024)
3-98498453-T-A		not specified	Uncertain significance (Dec 15, 2023)
3-98498455-T-C		not specified	Uncertain significance (Jan 04, 2024)
3-98498485-G-T		not specified	Uncertain significance (Aug 09, 2021)
3-98498497-C-T		not specified	Uncertain significance (Mar 01, 2023)
3-98498572-A-G		not specified	Uncertain significance (Nov 14, 2023)
3-98516669-C-G		not specified	Uncertain significance (Dec 12, 2023)
3-98516676-C-G			Uncertain significance (Aug 07, 2024)
3-98516793-C-T		not specified	Uncertain significance (Dec 07, 2021)
3-98516819-T-C		not specified	Uncertain significance (Apr 26, 2023)
3-98517157-C-T		not specified	Uncertain significance (Apr 17, 2023)
3-98518942-T-A		not specified	Uncertain significance (Mar 06, 2023)
3-98521169-T-C		not specified	Uncertain significance (Apr 07, 2022)
3-98521171-G-C		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLDND1	protein_coding	protein_coding	ENST00000437922	6	25155

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.164	0.834	125733	0	7	125740	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0900	155	158	0.980	0.00000833	1819
Missense in Polyphen		48	59.448	0.80743		702
Synonymous	-0.473	59	54.6	1.08	0.00000281	522
Loss of Function	2.61	4	14.8	0.270	8.59e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000194	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.836
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.641
• hipred: Y
• hipred_score: 0.592
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.505

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cldnd1

Gene ontology

• Cellular component: cell surface;integral component of membrane