PCDHGA2

protocadherin gamma subfamily A, 2, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141338760-141512975

Links

ENSG00000081853 ∙ NCBI:56113 ∙ OMIM:606289 ∙ HGNC:8700 ∙ Uniprot:Q9Y5H1 ∙ 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 PCDHGA2 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 PCDHGA2 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			55	6		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1	3	930	76	16	1026
Total	1	3	985	86	17

Variants in PCDHGA2

This is a list of pathogenic ClinVar variants found in the PCDHGA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141338984-C-A		not specified	Uncertain significance (Feb 12, 2024)
5-141338987-A-C		not specified	Uncertain significance (Jun 13, 2023)
5-141338997-A-G		not specified	Uncertain significance (Dec 28, 2022)
5-141339011-G-A		not specified	Uncertain significance (Apr 15, 2024)
5-141339012-T-C		not specified	Uncertain significance (Dec 14, 2023)
5-141339174-C-A		not specified	Uncertain significance (Oct 26, 2022)
5-141339330-A-G		not specified	Uncertain significance (May 13, 2024)
5-141339365-C-A		not specified	Uncertain significance (May 16, 2024)
5-141339396-T-C		not specified	Uncertain significance (May 22, 2023)
5-141339479-T-C		not specified	Uncertain significance (Jun 05, 2023)
5-141339482-G-C		not specified	Uncertain significance (Jan 18, 2022)
5-141339602-G-A		not specified	Uncertain significance (Oct 26, 2022)
5-141339624-G-T		not specified	Uncertain significance (Feb 10, 2022)
5-141339655-C-G		not specified	Uncertain significance (Nov 21, 2022)
5-141339764-A-G		not specified	Uncertain significance (Oct 12, 2021)
5-141339861-C-A		not specified	Uncertain significance (Aug 24, 2022)
5-141339974-G-A		not specified	Likely benign (Aug 12, 2021)
5-141339995-G-A		not specified	Uncertain significance (Mar 07, 2023)
5-141340031-A-G		not specified	Uncertain significance (Mar 29, 2022)
5-141340109-G-A		not specified	Uncertain significance (Jun 23, 2023)
5-141340109-G-T		not specified	Uncertain significance (Aug 14, 2023)
5-141340127-C-T		not specified	Uncertain significance (Jul 14, 2021)
5-141340187-A-C		not specified	Uncertain significance (Sep 20, 2023)
5-141340199-C-T		not specified	Uncertain significance (Jan 10, 2023)
5-141340317-C-T		not specified	Uncertain significance (Oct 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHGA2	protein_coding	protein_coding	ENST00000394576	4	174008

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.47e-16	0.0261	125601	0	147	125748	0.000585

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.145	580	570	1.02	0.0000391	6016
Missense in Polyphen		217	213.93	1.0144		2503
Synonymous	-0.0112	270	270	1.00	0.0000220	2025
Loss of Function	0.454	25	27.6	0.907	0.00000159	308

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00167	0.00164
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000707	0.000707
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000591	0.000589
Middle Eastern	0.000707	0.000707
South Asian	0.000719	0.000653
Other	0.000652	0.000652

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: 0.904
• rvis_EVS: 0.28
• rvis_percentile_EVS: 70.78

Haploinsufficiency Scores

• pHI: 0.0484
• hipred: N
• hipred_score: 0.227
• ghis: 0.519

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: Pcdhga2

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