PCDHA13

protocadherin alpha 13, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140882123-141012347

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.

• Inborn genetic diseases (105 variants)
• not provided (16 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.

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		7
missense			47	8		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			51	8		59
Total	0	0	98	23	0

Variants in PCDHA13

This is a list of pathogenic ClinVar variants found in the PCDHA13 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140882272-C-G		not specified	Likely benign (Jul 20, 2022)
5-140882282-G-T		not specified	Uncertain significance (Dec 21, 2022)
5-140882396-C-A		not specified	Uncertain significance (Jun 13, 2023)
5-140882408-G-C		not specified	Uncertain significance (Jul 12, 2023)
5-140882419-G-A		not specified	Uncertain significance (Feb 13, 2023)
5-140882450-C-A		not specified	Uncertain significance (Aug 22, 2023)
5-140882548-G-A		not specified	Uncertain significance (Sep 22, 2023)
5-140882554-T-G		not specified	Uncertain significance (Jul 07, 2023)
5-140882560-C-A			Likely benign (Sep 01, 2022)
5-140882588-A-G		not specified	Uncertain significance (Jul 06, 2021)
5-140882707-C-A		not specified	Uncertain significance (Dec 22, 2023)
5-140882752-A-G		not specified	Uncertain significance (Jan 19, 2024)
5-140882780-G-A		not specified	Uncertain significance (Jan 19, 2024)
5-140882813-C-A		not specified	Uncertain significance (Feb 28, 2024)
5-140882891-A-T		not specified	Uncertain significance (Dec 19, 2023)
5-140882894-G-A		not specified	Uncertain significance (Sep 23, 2023)
5-140882980-A-T		not specified	Uncertain significance (Dec 06, 2022)
5-140882987-C-T		not specified	Uncertain significance (Jun 30, 2023)
5-140883010-A-G		not specified	Uncertain significance (Jul 06, 2021)
5-140883025-G-A		not specified	Uncertain significance (Nov 10, 2022)
5-140883030-C-G		not specified	Uncertain significance (Jun 18, 2021)
5-140883072-T-A		not specified	Uncertain significance (May 17, 2023)
5-140883116-G-A		not specified	Uncertain significance (Feb 14, 2024)
5-140883117-G-T		not specified	Uncertain significance (Aug 28, 2023)
5-140883118-C-G		not specified	Uncertain significance (Jul 17, 2023)

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