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.

• not_specified (2131 variants)
• Inborn_genetic_diseases (96 variants)
• not_provided (60 variants)
• Neurodevelopmental_disorder_with_poor_growth_and_skeletal_anomalies (9 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (3 variants)
• Neurodevelopmental_disorder (1 variants)
• PCDHGC4-related_disorder (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. These statistics are base on transcript: NM_000018916.4. 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				6	1	7
missense			126	4		130
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	126	10	1

Highest pathogenic variant AF is 0.00000433829

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