PCDH9

protocadherin 9, the group of Non-clustered protocadherins

Basic information

Region (hg38): 13:66302833-67230445

Links

ENSG00000184226 ∙ NCBI:5101 ∙ OMIM:603581 ∙ HGNC:8661 ∙ Uniprot:Q9HC56 ∙ 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 PCDH9 gene.

• Inborn genetic diseases (28 variants)
• not provided (4 variants)
• PCDH9-related condition (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDH9 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					2	2
missense			31	2		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	2

Variants in PCDH9

This is a list of pathogenic ClinVar variants found in the PCDH9 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-66304735-T-C		not specified	Uncertain significance (Mar 16, 2022)
13-66304742-G-T			Likely benign (Aug 01, 2022)
13-66304816-C-G		not specified	Uncertain significance (May 31, 2022)
13-66304858-C-G		not specified	Uncertain significance (Nov 27, 2023)
13-66304864-T-C		not specified	Uncertain significance (Nov 30, 2021)
13-66304881-G-A		not specified	Uncertain significance (Jan 26, 2023)
13-66304887-A-C		not specified	Uncertain significance (Sep 15, 2021)
13-66304908-G-A		not specified	Uncertain significance (Oct 17, 2023)
13-66631254-G-A			Likely benign (Jan 01, 2024)
13-66631255-G-A		PCDH9-related disorder	Uncertain significance (Sep 26, 2023)
13-66631388-A-G			Benign (Aug 11, 2018)
13-66903544-G-A		not specified	Uncertain significance (Jun 06, 2023)
13-66903544-G-T		not specified	Uncertain significance (Jan 26, 2022)
13-66903591-G-T			Likely benign (Jan 01, 2023)
13-67225382-G-T		PCDH9-related disorder	Uncertain significance (Feb 15, 2024)
13-67225595-T-G		not specified	Uncertain significance (Nov 30, 2021)
13-67225606-C-A		not specified	Uncertain significance (Oct 17, 2023)
13-67225611-G-T		not specified	Uncertain significance (Nov 17, 2022)
13-67225617-C-T		not specified	Uncertain significance (Jun 22, 2021)
13-67225758-C-T		not specified	Uncertain significance (Jan 10, 2022)
13-67225780-G-C		not specified	Uncertain significance (Dec 26, 2023)
13-67225829-C-T		not specified	Uncertain significance (Jan 18, 2023)
13-67225969-C-T		not specified	Uncertain significance (May 17, 2023)
13-67225977-C-G		PCDH9-related disorder	Uncertain significance (Dec 09, 2022)
13-67226067-T-C		PCDH9-related disorder	Uncertain significance (Sep 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDH9	protein_coding	protein_coding	ENST00000544246	4	927502

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.809	0.191	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.33	495	664	0.746	0.0000349	8202
Missense in Polyphen		143	276.07	0.51799		3636
Synonymous	-0.335	264	257	1.03	0.0000145	2478
Loss of Function	4.25	6	31.9	0.188	0.00000178	425

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.0000621	0.0000615
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.212
• rvis_EVS: -0.13
• rvis_percentile_EVS: 44.09

Haploinsufficiency Scores

• pHI: 0.317
• hipred: Y
• hipred_score: 0.699
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.906

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdh9
• 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)

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules
• Cellular component: integral component of plasma membrane;growth cone;cell-cell contact zone
• Molecular function: calcium ion binding