PCDH7

protocadherin 7, the group of Non-clustered protocadherins|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 4:30720368-31146805

Links

ENSG00000169851 ∙ NCBI:5099 ∙ OMIM:602988 ∙ HGNC:8659 ∙ Uniprot:O60245 ∙ 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 PCDH7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDH7 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					6	6
missense			55	1	1	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	1	7

Variants in PCDH7

This is a list of pathogenic ClinVar variants found in the PCDH7 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-30721444-G-A		not specified	Uncertain significance (Dec 21, 2023)
4-30721518-G-C		not specified	Uncertain significance (Aug 12, 2021)
4-30721522-C-A		not specified	Uncertain significance (Apr 07, 2022)
4-30721550-C-T		not specified	Uncertain significance (Dec 17, 2023)
4-30721706-A-G		not specified	Uncertain significance (Jul 06, 2021)
4-30721781-C-T		not specified	Uncertain significance (Jul 27, 2021)
4-30721811-A-G		not specified	Likely benign (Apr 07, 2023)
4-30721830-C-G		not specified	Uncertain significance (May 04, 2022)
4-30721841-C-T		not specified	Uncertain significance (Mar 07, 2024)
4-30721874-C-T		not specified	Uncertain significance (Dec 14, 2023)
4-30721921-G-T		not specified	Uncertain significance (Sep 15, 2021)
4-30722030-G-T		not specified	Uncertain significance (Sep 17, 2021)
4-30722047-G-A		not specified	Uncertain significance (Dec 15, 2023)
4-30722104-G-T		not specified	Uncertain significance (Dec 17, 2021)
4-30722107-T-G		not specified	Uncertain significance (Mar 21, 2023)
4-30722140-C-T		not specified	Uncertain significance (Jun 30, 2022)
4-30722149-G-A		not specified	Uncertain significance (Mar 25, 2024)
4-30722288-C-G		not specified	Uncertain significance (Oct 14, 2023)
4-30722299-A-G		not specified	Uncertain significance (Aug 17, 2021)
4-30722305-C-T		not specified	Uncertain significance (Feb 05, 2024)
4-30722556-G-A			Benign (Dec 31, 2019)
4-30722597-A-C		not specified	Uncertain significance (Jun 18, 2021)
4-30722613-C-T			Benign (Jun 05, 2018)
4-30722665-A-G		not specified	Uncertain significance (Oct 13, 2021)
4-30722693-C-G		not specified	Uncertain significance (Jan 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDH7	protein_coding	protein_coding	ENST00000543491	3	426386

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.395	0.605	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	548	692	0.791	0.0000342	8168
Missense in Polyphen		153	269.73	0.56723		3064
Synonymous	-0.814	316	298	1.06	0.0000158	2597
Loss of Function	4.02	7	31.3	0.224	0.00000152	389

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000503	0.000489
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.0000358	0.0000352
Middle Eastern	0.000503	0.000489
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.231
• rvis_EVS: -1.5
• rvis_percentile_EVS: 3.6

Haploinsufficiency Scores

• pHI: 0.933
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.928

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdh7

Gene ontology

• Biological process: platelet degranulation;cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules
• Cellular component: plasma membrane;integral component of plasma membrane;platelet alpha granule membrane
• Molecular function: calcium ion binding