PCDH7

protein-coding

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

Gene summary

This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The gene encodes a protein with an extracellular domain containing 7 cadherin repeats. The gene product is an integral membrane protein that is thought to function in cell-cell recognition and adhesion. Alternative splicing yields isoforms with unique cytoplasmic tails. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001173523.2

Inheritance

—

ClinVar variants

U:136B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr4:30,720,369-31,146,805

External References & Databases

Ensembl (ENSG00000169851)

Transcript & Mutation Effects

hg38 • Region Span ~426.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PCDH7 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 136

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001173523.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		6 clinvar	7
missense			134 clinvar	3 clinvar	1 clinvar	138
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	136	3	7	146

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001173523.2	RefSeq	NP_001166994.1	3	MANE Select
ENST00000695919.1	Ensembl	ENSP00000512266.1	3	MANE Select
NM_002589.4	RefSeq	NP_002580.2	2	Standard
NM_032457.4	RefSeq	NP_115833.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Platelet degranulation
Response to elevated platelet cytosolic Ca2+
Platelet activation, signaling and aggregation
Hemostasis

Biological Process

platelet degranulation
cell adhesion
homophilic cell adhesion via plasma membrane adhesion molecules

Molecular Function

calcium ion binding

Cellular Component

plasma membrane
integral component of plasma membrane
platelet alpha granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000543491
Coding exons: 3
Length: 426386
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 21
Defined: 125748
p: 0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.95	548	692	0.791	0.0000342	8168
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00050	0.00049	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.231
RVIS EVS: -1.5
RVIS percentile EVS: 3.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.928

Gene Damage Prediction

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