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.

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.

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				1		1
missense			52			52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	1	0

Variants in PCDH17

This is a list of pathogenic ClinVar variants found in the PCDH17 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-57632638-C-T		not specified	Uncertain significance (Jun 10, 2022)
13-57632640-G-C		not specified	Uncertain significance (Jul 09, 2021)
13-57632665-G-T		not specified	Uncertain significance (Dec 16, 2022)
13-57632700-G-C		not specified	Uncertain significance (Nov 14, 2023)
13-57632727-T-C		not specified	Uncertain significance (Apr 24, 2024)
13-57632731-G-A		not specified	Uncertain significance (Dec 03, 2021)
13-57632763-C-T		not specified	Uncertain significance (Jan 10, 2022)
13-57632954-G-T		not specified	Uncertain significance (Jul 06, 2021)
13-57632958-G-C		not specified	Uncertain significance (Sep 14, 2023)
13-57632986-C-T		not specified	Uncertain significance (Jun 13, 2024)
13-57633021-C-G		not specified	Uncertain significance (Sep 26, 2023)
13-57633030-G-A		not specified	Uncertain significance (Jan 27, 2022)
13-57633040-G-C		not specified	Uncertain significance (Oct 30, 2023)
13-57633061-C-G		not specified	Uncertain significance (Jan 22, 2024)
13-57633111-G-C		not specified	Uncertain significance (Aug 13, 2021)
13-57633177-C-T		not specified	Uncertain significance (Feb 22, 2023)
13-57633213-C-G		not specified	Uncertain significance (Jan 31, 2024)
13-57633229-A-G		not specified	Uncertain significance (Dec 28, 2023)
13-57633233-C-G		not specified	Uncertain significance (Mar 08, 2024)
13-57633237-G-T		not specified	Uncertain significance (Apr 20, 2023)
13-57633447-G-A		not specified	Uncertain significance (Mar 14, 2023)
13-57633489-G-C			Uncertain significance (Apr 01, 2024)
13-57633494-G-A		not specified	Uncertain significance (Jul 11, 2023)
13-57633507-G-T		not specified	Uncertain significance (Nov 13, 2023)
13-57633600-G-C		not specified	Uncertain significance (Oct 27, 2022)

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