PCDHA6

protocadherin alpha 6, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140827957-141012347

Previous symbols: [ "CNRS2" ]

Links

ENSG00000081842 ∙ NCBI:56142 ∙ OMIM:606312 ∙ HGNC:8672 ∙ Uniprot:Q9UN73 ∙ 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 PCDHA6 gene.

• Inborn genetic diseases (426 variants)
• not provided (57 variants)
• not specified (1 variants)
• Thrombocytosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHA6 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				8		8
missense			45	3		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			356	72	1	429
Total	0	0	401	83	1

Variants in PCDHA6

This is a list of pathogenic ClinVar variants found in the PCDHA6 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140828207-C-A		not specified	Uncertain significance (Jun 24, 2022)
5-140828210-A-C		not specified	Uncertain significance (Mar 24, 2023)
5-140828269-G-A		not specified	Uncertain significance (Aug 09, 2021)
5-140828281-T-G		not specified	Uncertain significance (Sep 29, 2022)
5-140828334-T-G		not specified	Uncertain significance (Jan 23, 2023)
5-140828362-G-C		not specified	Uncertain significance (May 30, 2023)
5-140828384-G-A		not specified	Uncertain significance (Feb 27, 2024)
5-140828413-G-A		not specified	Uncertain significance (Jan 03, 2022)
5-140828424-C-A		not specified	Uncertain significance (Feb 10, 2022)
5-140828437-G-T		not specified	Uncertain significance (May 23, 2023)
5-140828492-C-G		not specified	Uncertain significance (Nov 23, 2021)
5-140828523-A-G			Likely benign (Jun 01, 2022)
5-140828575-G-T		not specified	Uncertain significance (Jun 12, 2023)
5-140828627-G-A		not specified	Uncertain significance (Dec 15, 2023)
5-140828666-T-C		not specified	Uncertain significance (Dec 03, 2021)
5-140828792-A-G		not specified	Uncertain significance (Apr 05, 2023)
5-140828799-T-C			Likely benign (Mar 01, 2022)
5-140828809-C-T		not specified	Uncertain significance (Dec 21, 2023)
5-140828843-T-C		not specified	Uncertain significance (Nov 22, 2022)
5-140828844-A-G		not specified	Uncertain significance (Nov 30, 2022)
5-140828869-A-G		not specified	Uncertain significance (Dec 08, 2021)
5-140828872-G-A		not specified	Uncertain significance (Dec 28, 2023)
5-140828940-C-G		not specified	Uncertain significance (Oct 17, 2023)
5-140828948-C-A		not specified	Uncertain significance (Mar 07, 2023)
5-140828984-A-T		not specified	Uncertain significance (Oct 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHA6	protein_coding	protein_coding	ENST00000529310	4	184367

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.62e-11	0.512	125646	0	102	125748	0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.01	658	589	1.12	0.0000422	6127
Missense in Polyphen		166	168.29	0.98639		1921
Synonymous	-2.59	344	288	1.19	0.0000256	2053
Loss of Function	1.29	20	27.2	0.734	0.00000143	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000906	0.000903
Ashkenazi Jewish	0.00	0.00
East Asian	0.000602	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000459	0.000457
Middle Eastern	0.000602	0.000598
South Asian	0.000563	0.000555
Other	0.000163	0.000163

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.

Recessive Scores

• pRec: 0.452

Intolerance Scores

• loftool: 0.805
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.18

Haploinsufficiency Scores

• pHI: 0.0666
• hipred: N
• hipred_score: 0.227
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdha6

Gene ontology

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