PCDHA10

protocadherin alpha 10, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140855883-141012347

Previous symbols: [ "CNRS8" ]

Links

ENSG00000250120 ∙ NCBI:56139 ∙ OMIM:606316 ∙ HGNC:8664 ∙ Uniprot:Q9Y5I2 ∙ 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 PCDHA10 gene.

• not_specified (794 variants)
• not_provided (44 variants)
• PCDHA13-related_disorder (2 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
• Prostate_cancer (1 variants)
• PCDHA12-related_condition (1 variants)
• Thrombocytosis (1 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 PCDHA10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018901.4. 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				10	1	11
missense			145	11		156
nonsense				1		1
start loss			1			1
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	147	22	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHA10	protein_coding	protein_coding	ENST00000307360	4	156335

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.09e-14	0.0870	125002	39	693	125734	0.00292

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.756	647	595	1.09	0.0000416	6079
Missense in Polyphen		213	192.84	1.1046		2161
Synonymous	-0.314	297	290	1.02	0.0000245	2060
Loss of Function	0.725	23	27.1	0.850	0.00000132	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00768	0.00738
Ashkenazi Jewish	0.00587	0.00517
East Asian	0.00169	0.00163
Finnish	0.0101	0.00961
European (Non-Finnish)	0.00192	0.00177
Middle Eastern	0.00169	0.00163
South Asian	0.00309	0.00294
Other	0.00248	0.00212

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: 0.925
• rvis_EVS: 1.61
• rvis_percentile_EVS: 95.93

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.172
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdha9
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;nervous system development
• Cellular component: extracellular region;integral component of plasma membrane
• Molecular function: calcium ion binding