PCDHA2

protocadherin alpha 2, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140794852-141012347

Links

ENSG00000204969 ∙ NCBI:56146 ∙ OMIM:606308 ∙ HGNC:8668 ∙ Uniprot:Q9Y5H9 ∙ 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 PCDHA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHA2 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				4	1	5
missense			57	6		63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			700	146	19	865
Total	0	0	757	156	20

Variants in PCDHA2

This is a list of pathogenic ClinVar variants found in the PCDHA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140795034-T-C		not specified	Uncertain significance (Jun 22, 2021)
5-140795059-G-C		not specified	Uncertain significance (Mar 06, 2023)
5-140795088-G-T		not specified	Uncertain significance (Mar 16, 2022)
5-140795130-C-A		not specified	Uncertain significance (Feb 06, 2023)
5-140795178-G-A		not specified	Uncertain significance (Sep 15, 2021)
5-140795271-A-G		not specified	Uncertain significance (Jun 22, 2024)
5-140795277-C-T		not specified	Uncertain significance (Nov 06, 2023)
5-140795293-T-C		not specified	Uncertain significance (May 28, 2024)
5-140795332-T-C		not specified	Uncertain significance (Dec 21, 2023)
5-140795338-A-T		not specified	Uncertain significance (Oct 26, 2022)
5-140795345-C-A		not specified	Uncertain significance (Sep 20, 2023)
5-140795367-A-G		not specified	Uncertain significance (May 23, 2023)
5-140795377-A-G		not specified	Uncertain significance (Jul 14, 2021)
5-140795382-A-C		not specified	Uncertain significance (Jan 03, 2024)
5-140795384-C-G			Likely benign (Dec 01, 2022)
5-140795385-C-G		not specified	Uncertain significance (Dec 15, 2022)
5-140795385-C-T		not specified	Uncertain significance (Apr 13, 2022)
5-140795494-T-A		not specified	Uncertain significance (Aug 17, 2022)
5-140795506-A-T		not specified	Uncertain significance (Dec 14, 2021)
5-140795591-T-A		not specified	Uncertain significance (Jul 05, 2023)
5-140795611-A-T		not specified	Uncertain significance (Feb 16, 2023)
5-140795650-T-G		not specified	Uncertain significance (Jul 20, 2022)
5-140795691-G-A		not specified	Uncertain significance (Apr 26, 2023)
5-140795725-A-G		not specified	Uncertain significance (Jun 03, 2024)
5-140795748-G-T		not specified	Uncertain significance (Apr 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHA2	protein_coding	protein_coding	ENST00000526136	4	217486

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.04e-23	0.000140	125196	5	547	125748	0.00220

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.742	630	580	1.09	0.0000422	6043
Missense in Polyphen		141	146.89	0.95991		1684
Synonymous	-1.56	311	278	1.12	0.0000246	2080
Loss of Function	-0.639	33	29.3	1.13	0.00000150	353

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00284	0.00277
Ashkenazi Jewish	0.000199	0.0000992
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000750	0.000712
Middle Eastern	0.000381	0.000381
South Asian	0.0133	0.0132
Other	0.000979	0.000978

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: 0.0947

Intolerance Scores

• loftool: 0.874
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.18

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.285

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.109

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdha2

Gene ontology

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