PCDHA4

protocadherin alpha 4, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140807037-141012347

Links

ENSG00000204967 ∙ NCBI:56144 ∙ OMIM:606310 ∙ HGNC:8670 ∙ Uniprot:Q9UN74 ∙ 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 PCDHA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHA4 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				7	1	8
missense			39	3		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			617	130	5	752
Total	0	0	656	140	6

Variants in PCDHA4

This is a list of pathogenic ClinVar variants found in the PCDHA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140807239-C-T		not specified	Uncertain significance (Sep 29, 2022)
5-140807332-G-T		not specified	Uncertain significance (Apr 07, 2023)
5-140807484-C-G		not specified	Uncertain significance (Nov 13, 2023)
5-140807506-G-C		not specified	Uncertain significance (Jun 07, 2022)
5-140807525-C-A		not specified	Uncertain significance (Dec 22, 2023)
5-140807569-G-C		not specified	Uncertain significance (Mar 16, 2022)
5-140807576-C-T		not specified	Uncertain significance (Oct 02, 2023)
5-140807577-G-T			Likely benign (Dec 01, 2022)
5-140807592-A-G			Likely benign (Dec 01, 2022)
5-140807604-C-T			Likely benign (Dec 01, 2022)
5-140807677-G-A		not specified	Uncertain significance (Jul 26, 2021)
5-140807809-A-G		not specified	Uncertain significance (Apr 25, 2022)
5-140807817-A-C		not specified	Uncertain significance (Jan 06, 2023)
5-140807822-T-C		not specified	Uncertain significance (Apr 17, 2024)
5-140807837-G-T		not specified	Uncertain significance (May 16, 2024)
5-140807845-C-T		not specified	Uncertain significance (Jun 18, 2021)
5-140807889-T-A		not specified	Uncertain significance (Feb 27, 2023)
5-140807933-T-C		not specified	Uncertain significance (Aug 16, 2022)
5-140808127-A-C		not specified	Uncertain significance (Apr 24, 2024)
5-140808133-T-C		not specified	Uncertain significance (Apr 19, 2024)
5-140808275-C-T		not specified	Uncertain significance (Feb 05, 2024)
5-140808284-G-A		not specified	Uncertain significance (May 03, 2024)
5-140808403-T-C		not specified	Uncertain significance (Dec 17, 2023)
5-140808495-G-C		not specified	Uncertain significance (Apr 26, 2023)
5-140808562-G-A		not specified	Uncertain significance (Jan 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHA4	protein_coding	protein_coding	ENST00000530339	4	205271

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.98e-23	0.000107	125517	11	220	125748	0.000919

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.774	630	578	1.09	0.0000412	6057
Missense in Polyphen		212	195.36	1.0851		2325
Synonymous	-0.398	288	280	1.03	0.0000243	2075
Loss of Function	-0.829	32	27.3	1.17	0.00000138	331

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00140	0.00139
Ashkenazi Jewish	0.00	0.00
East Asian	0.00610	0.00600
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000496	0.000457
Middle Eastern	0.00610	0.00600
South Asian	0.000905	0.000817
Other	0.000870	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent cell-adhesion protein involved in cells self-recognition and non-self discrimination. Thereby, it is involved in the establishment and maintenance of specific neuronal connections in the brain. {ECO:0000250|UniProtKB:O88689}.

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.956
• rvis_EVS: 0.83
• rvis_percentile_EVS: 88.13

Haploinsufficiency Scores

• pHI: 0.159
• hipred: N
• hipred_score: 0.227
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.572

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdha4

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;protein binding;identical protein binding