PCDHGA12

protocadherin gamma subfamily A, 12, the group of Clustered protocadherins

Basic information

Region (hg38): 5:141430507-141512975

Previous symbols: [ "CDH21" ]

Links

ENSG00000253159 ∙ NCBI:26025 ∙ OMIM:603059 ∙ HGNC:8699 ∙ Uniprot:O60330 ∙ 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 PCDHGA12 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 PCDHGA12 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	2	8
missense			68			68
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1	4	161	7	7	180
Total	1	4	229	13	9

Variants in PCDHGA12

This is a list of pathogenic ClinVar variants found in the PCDHGA12 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141430845-C-T		not specified	Uncertain significance (Oct 01, 2024)
5-141430910-G-A		not specified	Uncertain significance (Sep 25, 2024)
5-141430911-A-C		not specified	Uncertain significance (Dec 01, 2022)
5-141430950-T-G		not specified	Uncertain significance (Jul 19, 2023)
5-141431088-T-C		not specified	Uncertain significance (Dec 06, 2023)
5-141431115-T-C		not specified	Uncertain significance (Apr 08, 2022)
5-141431135-A-G		not specified	Uncertain significance (Jun 24, 2022)
5-141431167-T-G		not specified	Uncertain significance (Jul 12, 2023)
5-141431228-G-C		not specified	Uncertain significance (Dec 15, 2023)
5-141431262-A-G		not specified	Uncertain significance (Jul 19, 2023)
5-141431364-G-T		not specified	Uncertain significance (Nov 23, 2022)
5-141431375-G-T		not specified	Uncertain significance (Oct 03, 2023)
5-141431416-C-G		not specified	Uncertain significance (Dec 12, 2023)
5-141431423-C-A		not specified	Uncertain significance (May 18, 2022)
5-141431450-A-G		not specified	Uncertain significance (Sep 26, 2024)
5-141431457-T-C		not specified	Uncertain significance (Feb 15, 2023)
5-141431460-A-T		not specified	Uncertain significance (Jun 30, 2024)
5-141431473-C-G		not specified	Uncertain significance (Mar 31, 2023)
5-141431477-C-A		not specified	Uncertain significance (Jan 22, 2025)
5-141431537-C-A		not specified	Uncertain significance (Mar 28, 2024)
5-141431580-A-G		not specified	Uncertain significance (Jan 19, 2025)
5-141431672-G-A		not specified	Uncertain significance (Feb 14, 2024)
5-141431700-T-C		not specified	Uncertain significance (May 15, 2024)
5-141431744-G-A		not specified	Uncertain significance (Jan 29, 2024)
5-141431771-C-G		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHGA12	protein_coding	protein_coding	ENST00000252085	4	82362

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000142	0.991	125295	1	452	125748	0.00180

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.299	559	579	0.965	0.0000389	6016
Missense in Polyphen		197	205.3	0.95958		2315
Synonymous	1.04	258	280	0.921	0.0000224	2030
Loss of Function	2.36	14	27.3	0.513	0.00000141	313

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00603	0.00598
Ashkenazi Jewish	0.00	0.00
East Asian	0.000655	0.000653
Finnish	0.000323	0.000323
European (Non-Finnish)	0.00188	0.00187
Middle Eastern	0.000655	0.000653
South Asian	0.00332	0.00317
Other	0.00163	0.00163

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.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.625
• rvis_EVS: 0.23
• rvis_percentile_EVS: 68.57

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.263
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.459

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdhga12

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules
• Cellular component: integral component of plasma membrane;cell-cell junction
• Molecular function: calcium ion binding