PCDH17

protocadherin 17, the group of Non-clustered protocadherins

Basic information

Region (hg38): 13:57631744-57729311

Links

ENSG00000118946

∙ NCBI:27253 ∙ OMIM:611760 ∙ HGNC:14267 ∙ Uniprot:O14917 ∙ 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 PCDH17 gene.

not_specified (125 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDH17 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001040429.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			126 clinvar			126
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	126	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDH17	protein_coding	protein_coding	ENST00000377918	4	97502

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.641	0.359	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	591	690	0.856	0.0000363	7587
Missense in Polyphen		194	282.45	0.68684		3121
Synonymous	-2.46	349	295	1.18	0.0000173	2444
Loss of Function	4.01	6	29.6	0.203	0.00000136	341

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Potential calcium-dependent cell-adhesion protein.;

Recessive Scores

pRec: 0.116

Intolerance Scores

loftool: 0.149
rvis_EVS: -1.24
rvis_percentile_EVS: 5.49

Haploinsufficiency Scores

pHI: 0.590
hipred: Y
hipred_score: 0.809
ghis: 0.506

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.929

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pcdh17
Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Zebrafish Information Network

Gene name: pcdh17
Affected structure: retinal inner plexiform layer
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;adult behavior;negative regulation of synaptic transmission;synaptic membrane adhesion;presynaptic active zone assembly;regulation of synaptic vesicle clustering
Cellular component: integral component of plasma membrane;glutamatergic synapse;GABA-ergic synapse;integral component of postsynaptic membrane;integral component of presynaptic membrane
Molecular function: calcium ion binding;protein binding