PCDHA3

protocadherin alpha 3, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140801028-141012347

Links

ENSG00000255408 ∙ NCBI:56145 ∙ OMIM:606309 ∙ HGNC:8669 ∙ Uniprot:Q9Y5H8 ∙ 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 PCDHA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHA3 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				11	6	17
missense			44	4	7	55
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			656	135	7	798
Total	0	0	700	151	20

Variants in PCDHA3

This is a list of pathogenic ClinVar variants found in the PCDHA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140801219-G-A		not specified	Uncertain significance (Jan 07, 2022)
5-140801229-C-G		not specified	Uncertain significance (Nov 03, 2023)
5-140801286-A-G		not specified	Uncertain significance (Jul 20, 2021)
5-140801316-A-G		not specified	Uncertain significance (Apr 08, 2024)
5-140801379-C-A		PCDHA3-related disorder	Benign (Dec 27, 2019)
5-140801382-G-T		PCDHA3-related disorder	Benign (Dec 27, 2019)
5-140801491-G-A		PCDHA3-related disorder	Likely benign (Mar 07, 2019)
5-140801500-G-C		not specified	Uncertain significance (Aug 10, 2021)
5-140801509-C-T		PCDHA3-related disorder	Benign (Jul 23, 2019)
5-140801541-A-T		not specified	Uncertain significance (Aug 23, 2021)
5-140801553-T-G		not specified	Uncertain significance (Feb 28, 2023)
5-140801588-C-T		not specified	Uncertain significance (Apr 01, 2024)
5-140801608-A-G		PCDHA3-related disorder	Benign (Feb 20, 2019)
5-140801721-CTGAA-C		PCDHA3-related disorder	Likely benign (Mar 01, 2019)
5-140801771-C-G		not specified	Uncertain significance (Dec 19, 2022)
5-140801772-T-C		not specified	Uncertain significance (Jan 23, 2024)
5-140801780-G-C		not specified	Uncertain significance (Jul 09, 2021)
5-140801802-G-T		not specified	Uncertain significance (Jul 12, 2023)
5-140801845-T-A		not specified	Uncertain significance (Jan 19, 2024)
5-140801849-G-A		not specified	Uncertain significance (Sep 16, 2021)
5-140801899-T-C		PCDHA3-related disorder	Likely benign (Sep 17, 2019)
5-140801949-T-C		not specified	Uncertain significance (Dec 12, 2023)
5-140801979-T-C		not specified	Likely benign (Dec 20, 2021)
5-140801987-G-T		not specified	Uncertain significance (Jul 25, 2023)
5-140801999-G-T		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHA3	protein_coding	protein_coding	ENST00000522353	4	211147

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.40e-16	0.0335	123220	30	2498	125748	0.0101

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.690	632	585	1.08	0.0000416	6094
Missense in Polyphen		188	168.77	1.1139		1980
Synonymous	-1.64	319	284	1.12	0.0000244	2076
Loss of Function	0.534	25	28.1	0.891	0.00000146	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00802	0.00802
Ashkenazi Jewish	0.000794	0.000794
East Asian	0.00141	0.000870
Finnish	0.0352	0.0351
European (Non-Finnish)	0.0127	0.0127
Middle Eastern	0.00141	0.000870
South Asian	0.00101	0.000948
Other	0.0111	0.0110

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: 0.912
• rvis_EVS: -0.68
• rvis_percentile_EVS: 15.4

Haploinsufficiency Scores

• pHI: 0.0953
• hipred: N
• hipred_score: 0.220
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.131

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdha3

Gene ontology

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