PCDHA12

protocadherin alpha 12, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140875302-141012347

Links

ENSG00000251664 ∙ NCBI:56137 ∙ OMIM:606318 ∙ HGNC:8666 ∙ Uniprot:Q9UN75 ∙ 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 PCDHA12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHA12 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				5	1	6
missense			78	9		87
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			140	19		159
Total	0	0	218	33	1

Variants in PCDHA12

This is a list of pathogenic ClinVar variants found in the PCDHA12 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140875509-C-A		not specified	Uncertain significance (May 02, 2024)
5-140875510-G-T		not specified	Uncertain significance (Sep 07, 2022)
5-140875578-T-C		not specified	Uncertain significance (Jan 26, 2022)
5-140875579-A-C		not specified	Uncertain significance (Jan 26, 2022)
5-140875617-G-T		not specified	Uncertain significance (Sep 13, 2023)
5-140875651-T-C		not specified	Uncertain significance (Mar 29, 2022)
5-140875668-G-A		not specified	Uncertain significance (Apr 07, 2023)
5-140875680-A-G		not specified	Likely benign (Apr 07, 2023)
5-140875682-A-C		not specified	Uncertain significance (Apr 07, 2023)
5-140875683-C-G		not specified	Uncertain significance (Apr 07, 2023)
5-140875684-A-G		not specified	Likely benign (Apr 07, 2023)
5-140875735-C-G		not specified	Uncertain significance (Feb 07, 2023)
5-140875741-T-C		not specified	Uncertain significance (Oct 04, 2022)
5-140875746-C-T		not specified	Uncertain significance (Jan 03, 2024)
5-140875764-C-T		not specified	Uncertain significance (Jan 02, 2024)
5-140875771-C-T			Likely benign (Nov 01, 2023)
5-140875781-T-C			Likely benign (Nov 01, 2023)
5-140875816-A-C		not specified	Uncertain significance (May 05, 2023)
5-140875817-G-C		not specified	Uncertain significance (Sep 06, 2022)
5-140875833-G-A		not specified	Uncertain significance (Feb 02, 2022)
5-140875833-G-T		not specified	Uncertain significance (Aug 17, 2021)
5-140875843-A-G		not specified	Uncertain significance (Jan 24, 2024)
5-140875889-G-T		not specified	Uncertain significance (Dec 18, 2023)
5-140875890-G-A		not specified	Uncertain significance (Oct 12, 2021)
5-140875890-G-T		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHA12	protein_coding	protein_coding	ENST00000398631	4	136872

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.42e-13	0.126	125179	5	564	125748	0.00227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.337	608	585	1.04	0.0000414	6056
Missense in Polyphen		160	165.07	0.96926		1939
Synonymous	0.992	264	285	0.925	0.0000250	2046
Loss of Function	0.796	22	26.4	0.833	0.00000131	318

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00310	0.00302
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000718	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.000441	0.000422
Middle Eastern	0.000718	0.000707
South Asian	0.0140	0.0140
Other	0.00114	0.000978

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: 0.859
• rvis_EVS: 1.23
• rvis_percentile_EVS: 93.28

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.227
• ghis: 0.398

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: Pcdha10

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