PCDHGA11

protocadherin gamma subfamily A, 11, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141421047-141512975

Links

ENSG00000253873 ∙ NCBI:56105 ∙ OMIM:606298 ∙ HGNC:8698 ∙ Uniprot:Q9Y5H2 ∙ 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 PCDHGA11 gene.

• not_specified (405 variants)
• Inborn_genetic_diseases (96 variants)
• not_provided (25 variants)
• Neurodevelopmental_disorder_with_poor_growth_and_skeletal_anomalies (9 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 PCDHGA11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018914.3. 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				3	1	4
missense			102	6	1	109
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	102	9	2

Highest pathogenic variant AF is 0.00000433829

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHGA11	protein_coding	protein_coding	ENST00000398587	4	91074

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.27e-8	0.942	125597	0	144	125741	0.000573

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	498	570	0.874	0.0000343	6045
Missense in Polyphen		148	163.5	0.90519		1904
Synonymous	0.743	243	258	0.941	0.0000177	2013
Loss of Function	1.93	17	28.0	0.606	0.00000149	306

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00239	0.00238
Ashkenazi Jewish	0.000379	0.000298
East Asian	0.000390	0.000381
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000531	0.000501
Middle Eastern	0.000390	0.000381
South Asian	0.000306	0.000261
Other	0.00115	0.00114

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: 0.600
• rvis_EVS: 0.05
• rvis_percentile_EVS: 57.54

Haploinsufficiency Scores

• pHI: 0.325
• hipred: N
• hipred_score: 0.305
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhga11

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