PCDH10

protocadherin 10, the group of Non-clustered protocadherins

Basic information

Region (hg38): 4:133149294-133208606

Links

ENSG00000138650 ∙ NCBI:57575 ∙ OMIM:608286 ∙ HGNC:13404 ∙ Uniprot:Q9P2E7 ∙ 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 PCDH10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDH10 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				6	2	8
missense			45	2		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	45	9	2

Variants in PCDH10

This is a list of pathogenic ClinVar variants found in the PCDH10 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-133150174-A-T		not specified	Uncertain significance (Aug 04, 2021)
4-133150201-C-T		not specified	Uncertain significance (Jul 31, 2023)
4-133150247-A-G		not specified	Uncertain significance (Dec 18, 2023)
4-133150286-C-T		not specified	Uncertain significance (May 09, 2024)
4-133150428-G-C		not specified	Uncertain significance (Apr 26, 2024)
4-133150609-C-A		not specified	Uncertain significance (Mar 25, 2024)
4-133150669-G-A		not specified	Uncertain significance (Apr 25, 2023)
4-133150710-C-T			Benign (Jun 13, 2018)
4-133150765-G-A		not specified	Uncertain significance (Jan 22, 2024)
4-133150777-G-A		not specified	Uncertain significance (Apr 22, 2024)
4-133150817-C-G		not specified	Uncertain significance (Feb 28, 2024)
4-133150817-C-T		not specified	Uncertain significance (Jun 07, 2023)
4-133150891-G-C		not specified	Uncertain significance (Jan 02, 2024)
4-133150908-T-C			Likely benign (Oct 10, 2018)
4-133150985-A-G		not specified	Uncertain significance (Sep 01, 2021)
4-133151051-C-T		not specified	Uncertain significance (Dec 03, 2021)
4-133151118-G-A			Likely benign (Apr 03, 2018)
4-133151203-G-A		not specified	Uncertain significance (Dec 27, 2023)
4-133151257-C-G		not specified	Uncertain significance (May 31, 2023)
4-133151389-A-G		not specified	Uncertain significance (Apr 24, 2023)
4-133151399-C-T		not specified	Uncertain significance (Sep 27, 2021)
4-133151423-C-T			Likely benign (Jan 25, 2018)
4-133151430-C-A			Benign (Jul 09, 2018)
4-133151440-G-C		not specified	Uncertain significance (Mar 07, 2024)
4-133151446-C-T		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDH10	protein_coding	protein_coding	ENST00000264360	5	58887

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.891	0.109	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	520	594	0.875	0.0000289	6697
Missense in Polyphen		214	296.16	0.72258		3451
Synonymous	-1.37	280	252	1.11	0.0000126	2216
Loss of Function	4.41	6	33.6	0.178	0.00000164	354

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000244
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential calcium-dependent cell-adhesion protein.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.232
• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.46

Haploinsufficiency Scores

• pHI: 0.590
• hipred: Y
• hipred_score: 0.617
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.492

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdh10
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype

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