PCDH9

protocadherin 9, the group of Non-clustered protocadherins

Basic information

Region (hg38): 13:66302834-67230445

Links

ENSG00000184226NCBI:5101OMIM:603581HGNC:8661Uniprot:Q9HC56AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCDH9 gene.

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
clinvar
2
clinvar
4
missense
65
clinvar
4
clinvar
69
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 65 6 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)2278952
13-66304742-G-T Likely benign (Aug 01, 2022)2643836
13-66304816-C-G not specified Uncertain significance (May 31, 2022)2293386
13-66304858-C-G not specified Uncertain significance (Nov 27, 2023)3209262
13-66304864-T-C not specified Uncertain significance (Nov 30, 2021)2262685
13-66304881-G-A not specified Uncertain significance (Jan 26, 2023)2479630
13-66304887-A-C not specified Uncertain significance (Sep 15, 2021)2384065
13-66304908-G-A not specified Uncertain significance (Oct 17, 2023)3209261
13-66305008-C-G not specified Uncertain significance (Mar 25, 2024)3304634
13-66631254-G-A Likely benign (Jan 01, 2024)3024693
13-66631255-G-A PCDH9-related disorder Uncertain significance (Sep 26, 2023)2631068
13-66631279-C-T not specified Uncertain significance (Apr 08, 2024)3304635
13-66631303-G-T not specified Uncertain significance (Nov 08, 2024)3414835
13-66631342-C-T not specified Uncertain significance (Oct 04, 2024)3414833
13-66631388-A-G Benign (Aug 11, 2018)780154
13-66631401-C-T not specified Uncertain significance (Nov 09, 2024)3414836
13-66631404-C-T not specified Uncertain significance (Oct 01, 2024)3414827
13-66631405-G-A not specified Uncertain significance (May 23, 2024)3304633
13-66903544-G-A not specified Uncertain significance (Jun 06, 2023)2558219
13-66903544-G-T not specified Uncertain significance (Jan 26, 2022)2226352
13-66903545-T-C not specified Likely benign (Jun 13, 2024)3304631
13-66903591-G-T Likely benign (Jul 01, 2024)2643837
13-67225382-G-T PCDH9-related disorder Uncertain significance (Feb 15, 2024)3032070
13-67225488-A-G not specified Uncertain significance (Jun 16, 2024)3304639
13-67225575-C-G not specified Uncertain significance (Nov 25, 2024)3414826

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PCDH9protein_codingprotein_codingENST00000544246 4927502
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8090.1911257360111257470.0000437
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.334956640.7460.00003498202
Missense in Polyphen143276.070.517993636
Synonymous-0.3352642571.030.00001452478
Loss of Function4.25631.90.1880.00000178425

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002900.0000290
Ashkenazi Jewish0.000.00
East Asian0.00005450.0000544
Finnish0.00004670.0000462
European (Non-Finnish)0.00006210.0000615
Middle Eastern0.00005450.0000544
South Asian0.000.00
Other0.0001650.000163

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
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.906

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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