PCDH1

protocadherin 1, the group of Non-clustered protocadherins

Basic information

Region (hg38): 5:141853090-141879246

Links

ENSG00000156453 ∙ NCBI:5097 ∙ OMIM:603626 ∙ HGNC:8655 ∙ Uniprot:Q08174 ∙ 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 PCDH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDH1 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			59	5	1	65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	59	5	1

Variants in PCDH1

This is a list of pathogenic ClinVar variants found in the PCDH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141854067-G-A		not specified	Uncertain significance (Jan 26, 2023)
5-141854101-A-C		not specified	Uncertain significance (Apr 27, 2024)
5-141854110-T-C		not specified	Uncertain significance (Oct 05, 2023)
5-141854211-G-A		not specified	Uncertain significance (May 04, 2022)
5-141854213-T-G		not specified	Uncertain significance (Dec 01, 2022)
5-141854223-C-T		not specified	Uncertain significance (May 04, 2023)
5-141854232-G-A		not specified	Uncertain significance (Jun 07, 2024)
5-141854232-G-C		not specified	Uncertain significance (Sep 14, 2021)
5-141854233-G-C		not specified	Uncertain significance (Aug 20, 2024)
5-141854248-C-T		not specified	Uncertain significance (Sep 17, 2021)
5-141854325-C-A		not specified	Uncertain significance (Mar 01, 2023)
5-141854325-C-T		not specified	Uncertain significance (Nov 21, 2024)
5-141854379-T-G		not specified	Uncertain significance (Jun 26, 2024)
5-141854391-C-G		not specified	Uncertain significance (Nov 21, 2024)
5-141854406-G-A			Likely benign (May 09, 2018)
5-141857262-G-T		not specified	Uncertain significance (Nov 08, 2022)
5-141857305-T-C		not specified	Uncertain significance (Aug 02, 2023)
5-141863251-G-A		not specified	Uncertain significance (Feb 14, 2023)
5-141863284-T-A		not specified	Uncertain significance (Dec 15, 2022)
5-141863505-C-G		not specified	Uncertain significance (Aug 28, 2024)
5-141863641-T-C		not specified	Uncertain significance (May 20, 2024)
5-141863719-G-A		not specified	Uncertain significance (Sep 08, 2024)
5-141863771-G-A		not specified	Uncertain significance (Jan 31, 2024)
5-141863798-C-T		not specified	Uncertain significance (Oct 08, 2024)
5-141863836-G-A		not specified	Uncertain significance (Nov 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDH1	protein_coding	protein_coding	ENST00000287008	5	25874

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00162	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.08	504	740	0.681	0.0000468	7962
Missense in Polyphen		171	364.54	0.46909		3981
Synonymous	-0.118	320	317	1.01	0.0000201	2665
Loss of Function	4.75	3	32.0	0.0939	0.00000176	386

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000186	0.0000176
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in cell-cell interaction processes and in cell adhesion.

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.225
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.32

Haploinsufficiency Scores

• pHI: 0.862
• hipred: Y
• hipred_score: 0.837
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.582

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdh1

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;cell-cell signaling;nervous system development
• Cellular component: nucleus;nucleolus;plasma membrane;integral component of plasma membrane;cell-cell junction;cell junction;intracellular membrane-bounded organelle
• Molecular function: calcium ion binding