PCDHGA3

protocadherin gamma subfamily A, 3, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141343829-141512975

Links

ENSG00000254245 ∙ NCBI:56112 ∙ OMIM:606290 ∙ HGNC:8701 ∙ Uniprot:Q9Y5H0 ∙ 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 PCDHGA3 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 PCDHGA3 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				4	1	5
missense			58	3	1	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1	3	876	72	15	967
Total	1	3	934	79	17

Variants in PCDHGA3

This is a list of pathogenic ClinVar variants found in the PCDHGA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141344041-A-G		not specified	Uncertain significance (Jun 11, 2024)
5-141344106-G-A		not specified	Likely benign (Mar 01, 2023)
5-141344127-C-T		not specified	Uncertain significance (Feb 05, 2024)
5-141344220-G-C		not specified	Uncertain significance (Sep 01, 2021)
5-141344238-A-G		not specified	Uncertain significance (Jan 23, 2023)
5-141344253-C-G		not specified	Uncertain significance (Mar 01, 2024)
5-141344278-G-A		not specified	Uncertain significance (Feb 28, 2023)
5-141344292-G-C		not specified	Uncertain significance (Feb 28, 2023)
5-141344322-G-A		not specified	Uncertain significance (Jan 24, 2024)
5-141344348-A-C		not specified	Uncertain significance (Aug 02, 2022)
5-141344379-A-C		not specified	Uncertain significance (Mar 02, 2023)
5-141344443-A-G		not specified	Uncertain significance (Feb 16, 2023)
5-141344466-C-A		not specified	Uncertain significance (Dec 15, 2023)
5-141344493-A-C			Benign (Jan 18, 2019)
5-141344536-A-G		not specified	Uncertain significance (Jan 23, 2024)
5-141344574-G-A		not specified	Uncertain significance (Apr 04, 2024)
5-141344586-G-A		not specified	Uncertain significance (Jan 03, 2024)
5-141344602-A-G		not specified	Uncertain significance (May 31, 2023)
5-141344605-A-G		not specified	Uncertain significance (May 18, 2023)
5-141344788-G-T		not specified	Uncertain significance (Jan 03, 2022)
5-141344818-T-A		not specified	Uncertain significance (Jan 02, 2024)
5-141344905-T-C		not specified	Uncertain significance (Dec 20, 2023)
5-141344911-A-T		not specified	Uncertain significance (Feb 15, 2023)
5-141344984-T-G		not specified	Uncertain significance (Oct 16, 2023)
5-141344995-C-T		not specified	Uncertain significance (Jun 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHGA3	protein_coding	protein_coding	ENST00000253812	4	168946

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.61e-8	0.954	125251	3	490	125744	0.00196

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0616	572	576	0.993	0.0000380	6007
Missense in Polyphen		176	167.37	1.0516		1924
Synonymous	-1.16	297	273	1.09	0.0000211	2036
Loss of Function	1.97	16	27.1	0.591	0.00000147	300

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00291	0.00283
Ashkenazi Jewish	0.0209	0.0209
East Asian	0.000664	0.000653
Finnish	0.000185	0.000185
European (Non-Finnish)	0.00116	0.00113
Middle Eastern	0.000664	0.000653
South Asian	0.00206	0.00203
Other	0.00198	0.00196

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: 0.518
• rvis_EVS: 0.47
• rvis_percentile_EVS: 78.86

Haploinsufficiency Scores

• pHI: 0.181
• hipred: N
• hipred_score: 0.263
• ghis: 0.536

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	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pcdhga3

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;endosome to lysosome transport;lipid tube assembly involved in organelle fusion
• Cellular component: integral component of plasma membrane
• Molecular function: calcium ion binding