PCDHA13

protocadherin alpha 13, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140882124-141012347

Previous symbols: [ "CNRS5" ]

Links

ENSG00000239389 ∙ NCBI:56136 ∙ OMIM:606319 ∙ HGNC:8667 ∙ Uniprot:Q9Y5I0 ∙ 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 PCDHA13 gene.

• not_specified (359 variants)
• not_provided (18 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 PCDHA13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018904.3. 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				7	1	8
missense			139	11		150
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	139	18	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHA13	protein_coding	protein_coding	ENST00000289272	4	130137

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.45e-14	0.122	125649	0	99	125748	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.128	580	589	0.985	0.0000414	6089
Missense in Polyphen		155	157.15	0.98631		1839
Synonymous	1.14	265	290	0.915	0.0000252	2067
Loss of Function	0.892	24	29.2	0.822	0.00000150	342

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000632	0.000631
Ashkenazi Jewish	0.00	0.00
East Asian	0.000874	0.000870
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000292	0.000290
Middle Eastern	0.000874	0.000870
South Asian	0.00108	0.00108
Other	0.000163	0.000163

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: 0.773
• rvis_EVS: -0.52
• rvis_percentile_EVS: 20.94

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.227
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0725

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdha12

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