PCDHAC2

protocadherin alpha subfamily C, 2, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140966470-141012347

Links

ENSG00000243232 ∙ NCBI:56134 ∙ OMIM:606321 ∙ HGNC:8677 ∙ Uniprot:Q9Y5I4 ∙ 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 PCDHAC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHAC2 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			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	26	9	1

Variants in PCDHAC2

This is a list of pathogenic ClinVar variants found in the PCDHAC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140966862-G-C		not specified	Uncertain significance (May 24, 2024)
5-140966895-G-C		not specified	Uncertain significance (Oct 05, 2023)
5-140966962-G-C		not specified	Uncertain significance (Dec 13, 2023)
5-140967080-T-C		not specified	Uncertain significance (Dec 28, 2023)
5-140967172-G-A		not specified	Uncertain significance (May 27, 2022)
5-140967246-G-T			Likely benign (Feb 01, 2023)
5-140967448-A-G		not specified	Uncertain significance (Jul 09, 2021)
5-140967476-G-T		not specified	Uncertain significance (Jan 30, 2024)
5-140967542-A-G		not specified	Uncertain significance (Mar 07, 2023)
5-140967577-C-T		not specified	Uncertain significance (Aug 16, 2021)
5-140967672-C-G		not specified	Uncertain significance (Apr 09, 2024)
5-140967833-T-G		not specified	Uncertain significance (Dec 01, 2022)
5-140967927-C-G			Likely benign (Apr 01, 2023)
5-140967959-G-A		not specified	Uncertain significance (Jul 20, 2021)
5-140967961-A-C		not specified	Uncertain significance (Apr 07, 2022)
5-140968058-G-A		not specified	Uncertain significance (Aug 13, 2021)
5-140968115-C-T		not specified	Uncertain significance (Feb 03, 2022)
5-140968153-A-G		not specified	Uncertain significance (Oct 06, 2022)
5-140968280-C-T		not specified	Uncertain significance (Jan 24, 2024)
5-140968348-A-G		not specified	Uncertain significance (Jun 29, 2023)
5-140968355-G-C		not specified	Uncertain significance (Dec 13, 2022)
5-140968670-T-C		not specified	Uncertain significance (Jan 10, 2022)
5-140968677-G-A			Likely benign (Nov 01, 2023)
5-140968690-A-G		not specified	Uncertain significance (Apr 24, 2024)
5-140968789-G-A		not specified	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHAC2	protein_coding	protein_coding	ENST00000289269	4	46117

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.931	0.0689	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.72	462	579	0.799	0.0000305	6489
Missense in Polyphen		133	213.32	0.62349		2499
Synonymous	-0.398	253	245	1.03	0.0000132	2186
Loss of Function	4.28	5	30.6	0.164	0.00000184	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000233	0.000233
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000639	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

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: 0.108

Intolerance Scores

• loftool: 0.175
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.71

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.693
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.165

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhac2
• Phenotype: normal phenotype

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