PCDHGC3

protocadherin gamma subfamily C, 3, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141475947-141512977

Previous symbols: [ "PCDH2" ]

Links

ENSG00000240184 ∙ NCBI:5098 ∙ OMIM:603627 ∙ HGNC:8716 ∙ Uniprot:Q9UN70 ∙ 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 PCDHGC3 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 PCDHGC3 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	3	6
missense			59	2		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1	4	106	5	5	121
Total	1	4	165	10	8

Variants in PCDHGC3

This is a list of pathogenic ClinVar variants found in the PCDHGC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141476141-G-A		not specified	Uncertain significance (Jan 03, 2024)
5-141476294-A-T		not specified	Uncertain significance (Jun 13, 2023)
5-141476315-C-T		not specified	Uncertain significance (Jan 19, 2025)
5-141476340-G-A		not specified	Uncertain significance (Sep 04, 2024)
5-141476360-G-A		not specified	Uncertain significance (Mar 05, 2024)
5-141476382-A-G		not specified	Uncertain significance (Jan 17, 2024)
5-141476384-G-A		not specified	Uncertain significance (May 20, 2024)
5-141476412-G-T		not specified	Uncertain significance (Oct 12, 2022)
5-141476551-C-G		not specified	Uncertain significance (May 11, 2022)
5-141476574-G-A		not specified	Uncertain significance (Feb 19, 2025)
5-141476580-C-T		not specified	Uncertain significance (Sep 01, 2024)
5-141476610-G-A		not specified	Uncertain significance (Sep 06, 2022)
5-141476676-G-A		not specified	Uncertain significance (Jan 23, 2024)
5-141476714-C-G		not specified	Uncertain significance (Sep 27, 2021)
5-141476771-G-C		not specified	Uncertain significance (Jan 31, 2025)
5-141476780-C-T		not specified	Uncertain significance (Jan 24, 2023)
5-141476782-A-G			Benign (Jul 01, 2024)
5-141476856-C-A		not specified	Uncertain significance (Jan 29, 2024)
5-141476894-G-A		not specified	Uncertain significance (Dec 14, 2022)
5-141476903-G-A		not specified	Uncertain significance (Oct 20, 2024)
5-141476943-A-G		not specified	Uncertain significance (Sep 29, 2022)
5-141476955-T-C		not specified	Uncertain significance (Aug 28, 2024)
5-141476991-G-A		not specified	Uncertain significance (Aug 14, 2024)
5-141477037-G-T		not specified	Uncertain significance (Jun 29, 2023)
5-141477069-A-G		not specified	Uncertain significance (Feb 10, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHGC3	protein_coding	protein_coding	ENST00000308177	4	36963

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.125	0.875	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	472	567	0.833	0.0000330	6015
Missense in Polyphen		151	214.97	0.70243		2341
Synonymous	0.857	233	250	0.931	0.0000159	2073
Loss of Function	3.59	7	27.2	0.257	0.00000149	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.000163	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.000163	0.000163
South Asian	0.0000653	0.0000653
Other	0.000327	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: 0.443
• rvis_EVS: -1.55
• rvis_percentile_EVS: 3.25

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.464
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0980

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhgc3

Gene ontology

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