PCDHGA10

protocadherin gamma subfamily A, 10, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141412987-141512975

Links

ENSG00000253846 ∙ NCBI:56106 ∙ OMIM:606297 ∙ HGNC:8697 ∙ Uniprot:Q9Y5H3 ∙ 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 PCDHGA10 gene.

• Neurodevelopmental disorder with poor growth and skeletal anomalies (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHGA10 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	3	9
missense			38	3		41
nonsense				2		2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1	3	249	17	7	277
Total	1	3	287	28	10

Variants in PCDHGA10

This is a list of pathogenic ClinVar variants found in the PCDHGA10 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141413207-C-G			Likely benign (Jun 15, 2018)
5-141413272-C-T		not specified	Uncertain significance (May 20, 2024)
5-141413339-A-G		not specified	Uncertain significance (Sep 15, 2021)
5-141413407-C-G		not specified	Uncertain significance (Aug 17, 2022)
5-141413416-C-G		not specified	Uncertain significance (May 29, 2024)
5-141413426-G-T			Likely benign (Jul 15, 2018)
5-141413435-G-T		not specified	Uncertain significance (Mar 15, 2024)
5-141413524-A-T		not specified	Uncertain significance (Jul 26, 2021)
5-141413600-T-A		not specified	Uncertain significance (Oct 26, 2022)
5-141413624-T-C		not specified	Uncertain significance (Dec 15, 2023)
5-141413695-T-C		not specified	Uncertain significance (Nov 27, 2023)
5-141413752-G-A		not specified	Uncertain significance (Dec 01, 2022)
5-141413788-G-A		not specified	Uncertain significance (Dec 21, 2023)
5-141413794-G-A		not specified	Uncertain significance (Jun 28, 2022)
5-141413826-C-T			Benign (May 21, 2018)
5-141413906-C-T		not specified	Uncertain significance (Apr 17, 2024)
5-141413998-G-A		not specified	Uncertain significance (Mar 14, 2024)
5-141414015-A-T		not specified	Uncertain significance (Jun 21, 2022)
5-141414165-A-G			Likely benign (Jun 01, 2022)
5-141414170-T-C		not specified	Uncertain significance (Sep 16, 2021)
5-141414175-A-G		not specified	Uncertain significance (May 17, 2023)
5-141414189-G-C		not specified	Uncertain significance (May 18, 2022)
5-141414473-G-C		not specified	Uncertain significance (Mar 02, 2023)
5-141414479-C-G		not specified	Uncertain significance (Feb 14, 2024)
5-141414653-A-G		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHGA10	protein_coding	protein_coding	ENST00000398610	4	99804

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000117	0.988	124572	8	1168	125748	0.00469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	487	553	0.880	0.0000349	6055
Missense in Polyphen		135	153.09	0.88183		1861
Synonymous	0.270	250	256	0.978	0.0000190	2022
Loss of Function	2.29	14	26.8	0.522	0.00000141	317

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00516	0.00511
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.00155	0.00147
Finnish	0.00305	0.00305
European (Non-Finnish)	0.00496	0.00493
Middle Eastern	0.00155	0.00147
South Asian	0.0119	0.0117
Other	0.00443	0.00441

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.

Intolerance Scores

• loftool: 0.476
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.24

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.227
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhga10

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