PCDHGA8

protocadherin gamma subfamily A, 8, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141390157-141512975

Links

ENSG00000253767 ∙ NCBI:9708 ∙ OMIM:606295 ∙ HGNC:8706 ∙ Uniprot:Q9Y5G5 ∙ 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 PCDHGA8 gene.

• Neurodevelopmental disorder with poor growth and skeletal anomalies (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHGA8 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				3	1	4
missense			66	4		70
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1	3	406	43	11	464
Total	1	3	472	50	12

Variants in PCDHGA8

This is a list of pathogenic ClinVar variants found in the PCDHGA8 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141390219-T-C		not specified	Uncertain significance (Aug 13, 2021)
5-141390222-G-A		not specified	Uncertain significance (Sep 21, 2023)
5-141390225-G-A		not specified	Uncertain significance (Dec 19, 2022)
5-141390264-G-C		not specified	Uncertain significance (Apr 23, 2024)
5-141392830-G-A		not specified	Likely benign (May 21, 2024)
5-141392844-G-C		not specified	Uncertain significance (Oct 29, 2021)
5-141392850-C-A		not specified	Uncertain significance (Jan 30, 2024)
5-141392863-G-A		not specified	Uncertain significance (Mar 15, 2024)
5-141392976-G-A		not specified	Uncertain significance (Nov 14, 2023)
5-141392977-A-G		not specified	Uncertain significance (Feb 09, 2023)
5-141393015-T-A		not specified	Uncertain significance (Jun 07, 2024)
5-141393057-G-C		not specified	Uncertain significance (Sep 16, 2021)
5-141393093-G-A		not specified	Uncertain significance (Mar 14, 2024)
5-141393106-A-C		not specified	Uncertain significance (Oct 13, 2023)
5-141393139-T-A		not specified	Uncertain significance (Jun 18, 2024)
5-141393141-G-A		not specified	Uncertain significance (Mar 15, 2024)
5-141393173-A-C		not specified	Uncertain significance (Aug 22, 2023)
5-141393186-G-A		not specified	Uncertain significance (Feb 28, 2023)
5-141393196-A-G		not specified	Uncertain significance (Jun 28, 2022)
5-141393255-C-G		not specified	Uncertain significance (Jun 29, 2022)
5-141393255-C-T		not specified	Uncertain significance (May 10, 2022)
5-141393339-C-T		not specified	Uncertain significance (Feb 23, 2023)
5-141393354-G-A		not specified	Uncertain significance (Mar 28, 2024)
5-141393414-G-C		not specified	Uncertain significance (Jul 11, 2022)
5-141393453-G-A		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHGA8	protein_coding	protein_coding	ENST00000398604	4	120166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.28e-18	0.00560	102044	1502	22154	125700	0.0990

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0183	579	580	0.998	0.0000370	6028
Missense in Polyphen		173	167.4	1.0335		1871
Synonymous	1.02	250	271	0.921	0.0000201	2007
Loss of Function	0.0947	27	27.5	0.981	0.00000149	311

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.331	0.321
Ashkenazi Jewish	0.0948	0.0932
East Asian	0.106	0.103
Finnish	0.0569	0.0570
European (Non-Finnish)	0.0795	0.0787
Middle Eastern	0.106	0.103
South Asian	0.117	0.116
Other	0.0947	0.0930

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: 0.627
• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.77

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.227
• ghis: 0.406

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	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pcdhga8

Gene ontology

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