CDH17

cadherin 17, the group of 7D cadherins

Basic information

Region (hg38): 8:94127161-94217303

Links

ENSG00000079112 ∙ NCBI:1015 ∙ OMIM:603017 ∙ HGNC:1756 ∙ Uniprot:Q12864 ∙ 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 CDH17 gene.

• Inborn genetic diseases (28 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH17 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	4
missense			28	2	3	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	29	4	5

Variants in CDH17

This is a list of pathogenic ClinVar variants found in the CDH17 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-94128275-C-T		not specified	Uncertain significance (Dec 14, 2022)
8-94128296-C-T		not specified	Uncertain significance (Dec 12, 2023)
8-94130659-C-A		not specified	Uncertain significance (May 31, 2022)
8-94130660-T-C			Benign/Likely benign (Apr 01, 2022)
8-94130728-T-C		not specified	Uncertain significance (Oct 25, 2022)
8-94130909-G-A		not specified	Uncertain significance (Dec 18, 2023)
8-94130944-T-G			Benign (Jul 15, 2020)
8-94130955-A-G			Likely benign (Dec 14, 2018)
8-94145957-T-C		not specified	Uncertain significance (Jul 14, 2023)
8-94145974-G-A			Benign (May 31, 2018)
8-94145999-C-T		not specified	Uncertain significance (Sep 12, 2023)
8-94146000-G-A		not specified	Uncertain significance (Apr 15, 2022)
8-94146054-T-A		not specified	Uncertain significance (May 27, 2022)
8-94146062-T-C		not specified	Uncertain significance (Dec 05, 2023)
8-94146071-A-G		not specified	Uncertain significance (Aug 16, 2021)
8-94146120-C-T		not specified	Uncertain significance (May 03, 2023)
8-94148752-G-C		not specified	Uncertain significance (Jan 26, 2023)
8-94148783-C-T		not specified	Uncertain significance (Jul 30, 2023)
8-94148852-T-C		not specified	Uncertain significance (Jun 24, 2022)
8-94151866-A-G			Uncertain significance (Oct 01, 2018)
8-94151907-C-G		not specified	Uncertain significance (Nov 07, 2023)
8-94151956-C-T		not specified	Uncertain significance (Dec 11, 2023)
8-94151998-T-A		not specified	Likely benign (Feb 26, 2024)
8-94152028-T-C		not specified	Uncertain significance (Oct 03, 2022)
8-94152088-C-G		not specified	Uncertain significance (May 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH17	protein_coding	protein_coding	ENST00000027335	17	90133

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.42e-14	0.691	125582	0	164	125746	0.000652

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.351	438	459	0.954	0.0000238	5469
Missense in Polyphen		120	140.91	0.85158		1813
Synonymous	-0.801	185	172	1.08	0.00000950	1620
Loss of Function	1.74	27	38.7	0.698	0.00000197	464

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00256	0.00256
Ashkenazi Jewish	0.000696	0.000695
East Asian	0.000658	0.000653
Finnish	0.0000932	0.0000924
European (Non-Finnish)	0.000336	0.000334
Middle Eastern	0.000658	0.000653
South Asian	0.00167	0.00167
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. LI-cadherin may have a role in the morphological organization of liver and intestine. Involved in intestinal peptide transport. {ECO:0000269|PubMed:8153632}.
• Pathway: Gastric cancer - Homo sapiens (human);Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.895
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.25

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.386

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh17
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: cell morphogenesis;germinal center B cell differentiation;marginal zone B cell differentiation;oligopeptide transport;cell-cell junction assembly;cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;integrin-mediated signaling pathway;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;positive regulation of integrin activation by cell surface receptor linked signal transduction;adherens junction organization;oligopeptide transmembrane transport;cell-cell adhesion mediated by cadherin;spleen development;cell-cell adhesion
• Cellular component: nucleus;plasma membrane;cell-cell adherens junction;cell surface;integral component of membrane;basolateral plasma membrane;catenin complex;cell junction
• Molecular function: integrin binding;transporter activity;proton-dependent oligopeptide secondary active transmembrane transporter activity;calcium ion binding;cytoskeletal protein binding;protein homodimerization activity;cadherin binding