PCDHGC5

protocadherin gamma subfamily C, 5, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141489081-141512975

Links

ENSG00000240764 ∙ NCBI:56097 ∙ OMIM:606306 ∙ HGNC:8718 ∙ Uniprot:Q9Y5F6 ∙ 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 PCDHGC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHGC5 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	6	9
missense			56	3		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	6	6

Variants in PCDHGC5

This is a list of pathogenic ClinVar variants found in the PCDHGC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141489271-G-A		not specified	Uncertain significance (Feb 27, 2023)
5-141489314-G-C		not specified	Uncertain significance (Jan 27, 2025)
5-141489335-G-A		not specified	Uncertain significance (Aug 30, 2022)
5-141489425-G-A		not specified	Uncertain significance (Feb 22, 2025)
5-141489458-G-A		not specified	Likely benign (Oct 22, 2021)
5-141489478-A-G		not specified	Likely benign (Jul 27, 2024)
5-141489557-T-C		not specified	Uncertain significance (Dec 27, 2023)
5-141489592-C-T		not specified	Uncertain significance (Mar 01, 2024)
5-141489593-G-A		not specified	Uncertain significance (Jul 06, 2021)
5-141489661-C-T		not specified	Uncertain significance (Dec 20, 2022)
5-141489662-G-C		not specified	Uncertain significance (Sep 29, 2023)
5-141489719-C-T		not specified	Uncertain significance (Nov 02, 2023)
5-141489733-A-C		not specified	Uncertain significance (Jan 08, 2024)
5-141489760-C-T		not specified	Uncertain significance (Dec 16, 2023)
5-141489791-C-T		not specified	Uncertain significance (Sep 23, 2023)
5-141489878-C-T		not specified	Uncertain significance (Jan 21, 2025)
5-141489905-G-A		not specified	Likely benign (Dec 15, 2023)
5-141489924-C-G		not specified	Uncertain significance (Sep 29, 2022)
5-141489947-A-G		not specified	Uncertain significance (Jun 18, 2021)
5-141489969-A-T		not specified	Uncertain significance (Aug 04, 2023)
5-141489994-C-A		not specified	Uncertain significance (Nov 21, 2024)
5-141490130-C-A		not specified	Uncertain significance (Dec 05, 2022)
5-141490150-G-A		not specified	Uncertain significance (Apr 06, 2024)
5-141490181-G-A		not specified	Uncertain significance (Apr 07, 2022)
5-141490207-C-G		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHGC5	protein_coding	protein_coding	ENST00000252087	4	23739

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000883	0.997	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	461	564	0.817	0.0000355	6080
Missense in Polyphen		165	216.84	0.76094		2430
Synonymous	2.35	195	242	0.807	0.0000147	2094
Loss of Function	2.60	13	27.8	0.468	0.00000162	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000416	0.000416
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000276	0.000272
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000273	0.000264
Middle Eastern	0.000276	0.000272
South Asian	0.000131	0.000131
Other	0.000326	0.000326

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: 0.101

Intolerance Scores

• loftool: 0.514
• rvis_EVS: -1.46
• rvis_percentile_EVS: 3.82

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.406
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.225

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhgc5

Gene ontology

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