PCDHA1

protocadherin alpha 1, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140786135-141012347

Links

ENSG00000204970 ∙ NCBI:56147 ∙ OMIM:606307 ∙ HGNC:8663 ∙ Uniprot:Q9Y5I3 ∙ 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 PCDHA1 gene.

• Inborn genetic diseases (614 variants)
• not provided (71 variants)
• not specified (1 variants)
• Thrombocytosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHA1 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			42	7		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			536	95	2	633
Total	0	0	578	106	3

Variants in PCDHA1

This is a list of pathogenic ClinVar variants found in the PCDHA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140786295-T-A		not specified	Uncertain significance (Feb 14, 2023)
5-140786298-T-G		not specified	Uncertain significance (Aug 13, 2021)
5-140786313-G-A		not specified	Uncertain significance (Jul 25, 2023)
5-140786325-G-T		not specified	Uncertain significance (Aug 17, 2021)
5-140786341-G-T		not specified	Uncertain significance (Apr 11, 2023)
5-140786399-G-C		not specified	Uncertain significance (Aug 02, 2021)
5-140786424-T-C		not specified	Uncertain significance (Feb 06, 2023)
5-140786581-G-C		not specified	Uncertain significance (Feb 06, 2023)
5-140786586-G-C		not specified	Uncertain significance (May 05, 2023)
5-140786609-G-A		not specified	Uncertain significance (Jan 24, 2023)
5-140786612-T-G		not specified	Likely benign (Feb 03, 2022)
5-140786619-C-T		not specified	Likely benign (Feb 03, 2022)
5-140786637-T-C		not specified	Uncertain significance (Sep 22, 2023)
5-140786643-A-T		not specified	Uncertain significance (Aug 21, 2023)
5-140786647-G-A			Benign (Nov 15, 2018)
5-140786691-G-C		not specified	Uncertain significance (Sep 18, 2023)
5-140786747-C-T		not specified	Uncertain significance (Jan 26, 2022)
5-140786774-A-C		not specified	Uncertain significance (Aug 04, 2023)
5-140786787-C-A		not specified	Uncertain significance (Oct 25, 2022)
5-140786811-C-T		not specified	Uncertain significance (Jan 20, 2023)
5-140786858-A-C		not specified	Uncertain significance (Sep 30, 2021)
5-140786904-C-T		not specified	Uncertain significance (Dec 31, 2023)
5-140787122-G-A		not specified	Uncertain significance (Dec 16, 2023)
5-140787150-G-A		not specified	Likely benign (Oct 12, 2021)
5-140787204-T-C		not specified	Uncertain significance (Feb 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHA1	protein_coding	protein_coding	ENST00000504120	4	226054

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.00e-8	0.967	125675	1	72	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.334	603	580	1.04	0.0000406	6084
Missense in Polyphen		126	131.07	0.96134		1511
Synonymous	-0.628	294	281	1.05	0.0000239	2073
Loss of Function	2.06	16	27.7	0.577	0.00000142	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000530	0.000530
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000291	0.000273
Middle Eastern	0.000544	0.000544
South Asian	0.000464	0.000425
Other	0.000490	0.000489

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: 0.720
• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.55

Haploinsufficiency Scores

• pHI: 0.0876
• hipred: N
• hipred_score: 0.296
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.107

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdha1
• Phenotype: normal phenotype

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;nervous system development
• Cellular component: extracellular region;endoplasmic reticulum;integral component of plasma membrane
• Molecular function: calcium ion binding