CLDND2

claudin domain containing 2

Basic information

Region (hg38): 19:51367098-51369003

Links

ENSG00000160318 ∙ NCBI:125875 ∙ ∙ HGNC:28511 ∙ Uniprot:Q8NHS1 ∙ 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 CLDND2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDND2 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				1		1
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	15	1	0

Variants in CLDND2

This is a list of pathogenic ClinVar variants found in the CLDND2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51367175-G-A			Likely benign (Feb 01, 2023)
19-51367458-C-T			Benign (Jul 01, 2023)
19-51367481-C-G		not specified	Uncertain significance (Oct 02, 2023)
19-51367513-A-C		not specified	Uncertain significance (Jun 26, 2024)
19-51367912-G-C		not specified	Uncertain significance (Dec 20, 2023)
19-51367931-C-T		not specified	Uncertain significance (Jun 02, 2024)
19-51367958-C-T		not specified	Uncertain significance (Mar 08, 2025)
19-51368414-C-A		not specified	Uncertain significance (Jul 28, 2024)
19-51368417-G-T		not specified	Uncertain significance (Feb 10, 2022)
19-51368421-T-C		not specified	Uncertain significance (Nov 25, 2024)
19-51368481-G-A		not specified	Uncertain significance (Dec 21, 2023)
19-51368490-A-T		not specified	Uncertain significance (Mar 24, 2023)
19-51368508-G-C		not specified	Uncertain significance (Jun 21, 2023)
19-51368519-A-T		not specified	Uncertain significance (Aug 12, 2024)
19-51368544-T-G		not specified	Uncertain significance (Sep 26, 2023)
19-51368562-T-C		not specified	Uncertain significance (Jul 13, 2022)
19-51368565-G-A		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLDND2	protein_coding	protein_coding	ENST00000291715	4	1906

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000366	0.212	125604	2	130	125736	0.000525

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.408	87	98.4	0.884	0.00000463	1063
Missense in Polyphen		46	38.008	1.2103		369
Synonymous	-0.466	46	42.1	1.09	0.00000198	339
Loss of Function	-0.170	8	7.50	1.07	3.22e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000342	0.000339
Ashkenazi Jewish	0.00	0.00
East Asian	0.000665	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.0000923	0.0000879
Middle Eastern	0.000665	0.000653
South Asian	0.00361	0.00324
Other	0.000352	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.404
• rvis_EVS: 0.79
• rvis_percentile_EVS: 87.4

Haploinsufficiency Scores

• pHI: 0.245
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.320

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cldnd2

Gene ontology

• Cellular component: plasma membrane;integral component of membrane