PCDHA8

protocadherin alpha 8, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140841186-141012347

Links

ENSG00000204962 ∙ NCBI:56140 ∙ OMIM:606314 ∙ HGNC:8674 ∙ Uniprot:Q9Y5H6 ∙ 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 PCDHA8 gene.

• Inborn genetic diseases (344 variants)
• not provided (48 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 PCDHA8 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				5		5
missense			36	10		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			285	57	1	343
Total	0	0	321	72	1

Variants in PCDHA8

This is a list of pathogenic ClinVar variants found in the PCDHA8 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140841325-G-A			Likely benign (Feb 01, 2023)
5-140841359-G-T		not specified	Uncertain significance (Dec 21, 2023)
5-140841377-T-C		not specified	Uncertain significance (Aug 11, 2022)
5-140841444-C-A		not specified	Uncertain significance (Jun 01, 2023)
5-140841491-C-A		not specified	Uncertain significance (Jun 06, 2023)
5-140841535-C-G		not specified	Likely benign (Jan 04, 2022)
5-140841560-A-G		not specified	Uncertain significance (Dec 17, 2023)
5-140841577-G-A		not specified	Uncertain significance (Dec 06, 2022)
5-140841596-G-T		not specified	Uncertain significance (Aug 04, 2023)
5-140841611-G-A		not specified	Uncertain significance (Oct 05, 2022)
5-140841641-A-T		not specified	Uncertain significance (Nov 16, 2021)
5-140841673-C-T		not specified	Uncertain significance (Sep 20, 2023)
5-140841776-T-G		not specified	Uncertain significance (Apr 04, 2023)
5-140841817-T-G		not specified	Likely benign (Jan 07, 2022)
5-140841933-C-A		not specified	Likely benign (May 25, 2022)
5-140841965-C-T		not specified	Uncertain significance (Jun 30, 2022)
5-140842039-C-T		not specified	Uncertain significance (Dec 19, 2023)
5-140842101-A-G			Likely benign (Mar 01, 2022)
5-140842178-A-C		not specified	Likely benign (Nov 08, 2021)
5-140842180-A-G		not specified	Uncertain significance (Nov 08, 2021)
5-140842286-C-T		not specified	Uncertain significance (Feb 12, 2024)
5-140842341-T-C			Likely benign (May 01, 2022)
5-140842523-T-A		not specified	Uncertain significance (Oct 12, 2021)
5-140842555-G-T		not specified	Uncertain significance (Dec 21, 2022)
5-140842580-C-G		not specified	Uncertain significance (Jun 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHA8	protein_coding	protein_coding	ENST00000531613	4	171023

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.29e-18	0.00531	125192	10	546	125748	0.00221

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.40	689	593	1.16	0.0000434	6081
Missense in Polyphen		125	131.25	0.95235		1436
Synonymous	-1.01	310	288	1.08	0.0000255	2069
Loss of Function	0.151	28	28.9	0.970	0.00000159	324

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00165	0.00163
Ashkenazi Jewish	0.00191	0.00179
East Asian	0.00163	0.00163
Finnish	0.00264	0.00264
European (Non-Finnish)	0.00311	0.00302
Middle Eastern	0.00163	0.00163
South Asian	0.00160	0.00157
Other	0.00246	0.00228

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: 0.904
• rvis_EVS: 1.88
• rvis_percentile_EVS: 97.23

Haploinsufficiency Scores

• pHI: 0.0881
• hipred: N
• hipred_score: 0.227
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.117

Gene Damage Prediction

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

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