PCDHAC1

protocadherin alpha subfamily C, 1, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140926299-141012347

Links

ENSG00000248383 ∙ NCBI:56135 ∙ OMIM:606320 ∙ HGNC:8676 ∙ Uniprot:Q9H158 ∙ 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 PCDHAC1 gene.

• not_specified (216 variants)
• not_provided (12 variants)
• PCDHA13-related_disorder (2 variants)
• Hirschsprung_disease,_susceptibility_to,_1 (1 variants)
• PCDHA9-related_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHAC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018898.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	1	5
missense			118	9		127
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	118	13	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHAC1	protein_coding	protein_coding	ENST00000253807	4	85628

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.57e-11	0.673	125449	0	299	125748	0.00119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00543	552	552	1.00	0.0000296	6227
Missense in Polyphen		162	151.4	1.07		1856
Synonymous	1.40	205	232	0.883	0.0000131	2079
Loss of Function	1.47	20	28.5	0.702	0.00000164	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00506	0.00499
Ashkenazi Jewish	0.000498	0.000496
East Asian	0.000381	0.000381
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.00127	0.00127
Middle Eastern	0.000381	0.000381
South Asian	0.000490	0.000490
Other	0.00115	0.00114

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: 0.976
• rvis_EVS: 1.23
• rvis_percentile_EVS: 93.27

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.180
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.259

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhac1
• 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