PCDHA9

protocadherin alpha 9, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140847772-141012347

Links

ENSG00000204961 ∙ NCBI:9752 ∙ OMIM:606315 ∙ HGNC:8675 ∙ Uniprot:Q9Y5H5 ∙ 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 PCDHA9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHA9 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				27	4	31
missense			65	21	1	87
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			330	57	1	388
Total	0	0	395	106	6

Variants in PCDHA9

This is a list of pathogenic ClinVar variants found in the PCDHA9 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140848526-G-T		not specified	Uncertain significance (Jun 21, 2023)
5-140848579-C-A		PCDHA9-related disorder	Likely benign (Sep 24, 2020)
5-140848597-C-G		PCDHA9-related disorder	Likely benign (Dec 01, 2022)
5-140848603-G-C		PCDHA9-related disorder	Likely benign (Dec 01, 2022)
5-140848609-A-G		PCDHA9-related disorder	Likely benign (Sep 25, 2020)
5-140848612-C-T		PCDHA9-related disorder	Likely benign (Sep 25, 2020)
5-140848613-G-A		PCDHA9-related disorder	Likely benign (Sep 25, 2020)
5-140848618-C-T		PCDHA9-related disorder	Likely benign (Jul 01, 2023)
5-140848620-G-A		not specified	Uncertain significance (Jan 10, 2022)
5-140848623-C-A		PCDHA9-related disorder • not specified	Uncertain significance (May 30, 2023)
5-140848658-G-C		not specified	Uncertain significance (Nov 28, 2023)
5-140848667-G-C		not specified	Uncertain significance (Sep 22, 2022)
5-140848680-G-T		not specified	Uncertain significance (Feb 24, 2022)
5-140848687-C-G		PCDHA9-related disorder	Likely benign (Sep 30, 2020)
5-140848706-C-T		not specified	Uncertain significance (Mar 01, 2024)
5-140848714-C-T			Likely benign (Jul 01, 2024)
5-140848728-A-G		not specified	Uncertain significance (Apr 09, 2024)
5-140848734-A-G		not specified	Uncertain significance (May 14, 2024)
5-140848773-A-T		not specified	Uncertain significance (Mar 06, 2023)
5-140848781-T-G			Likely benign (Jul 01, 2023)
5-140848794-C-T		not specified	Uncertain significance (Apr 07, 2023)
5-140848825-A-G		PCDHA9-related disorder	Likely benign (Sep 24, 2020)
5-140848828-C-A		PCDHA9-related disorder	Likely benign (Sep 24, 2020)
5-140848832-C-G		not specified	Uncertain significance (Jun 06, 2023)
5-140848851-T-C		not specified	Uncertain significance (Mar 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHA9	protein_coding	protein_coding	ENST00000532602	4	164882

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.89e-24	0.0000515	125447	26	275	125748	0.00120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.55	678	573	1.18	0.0000426	6065
Missense in Polyphen		233	209.71	1.111		2467
Synonymous	-1.60	312	278	1.12	0.0000252	2062
Loss of Function	-0.991	33	27.4	1.20	0.00000142	322

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0126	0.0117
Ashkenazi Jewish	0.000202	0.000198
East Asian	0.000490	0.000489
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000376	0.000325
Middle Eastern	0.000490	0.000489
South Asian	0.000987	0.000915
Other	0.000825	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Intolerance Scores

• loftool: 0.893
• rvis_EVS: 1.5
• rvis_percentile_EVS: 95.39

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.227

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.161

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Pcdha8

Gene ontology

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