PCDHA7

protocadherin alpha 7, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140834247-141012347

Previous symbols: [ "CNRS4" ]

Links

ENSG00000204963 ∙ NCBI:56141 ∙ OMIM:606313 ∙ HGNC:8673 ∙ Uniprot:Q9UN72 ∙ 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 PCDHA7 gene.

• Inborn genetic diseases (381 variants)
• not provided (51 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 PCDHA7 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		5
missense			35	5		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			321	67	1	389
Total	0	0	356	77	1

Variants in PCDHA7

This is a list of pathogenic ClinVar variants found in the PCDHA7 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140834387-G-A		not specified	Uncertain significance (Dec 19, 2022)
5-140834561-G-A		not specified	Uncertain significance (Feb 28, 2024)
5-140834637-T-C		not specified	Uncertain significance (Dec 18, 2023)
5-140834657-C-A		not specified	Uncertain significance (Aug 02, 2023)
5-140834666-C-G		not specified	Uncertain significance (Jul 08, 2022)
5-140834715-A-T		not specified	Uncertain significance (Aug 14, 2023)
5-140834955-C-T		not specified	Uncertain significance (Oct 26, 2022)
5-140835028-C-T			Likely benign (Mar 01, 2022)
5-140835250-A-G		not specified	Uncertain significance (Apr 04, 2023)
5-140835282-G-T		not specified	Uncertain significance (May 26, 2022)
5-140835306-T-C		not specified	Uncertain significance (Oct 17, 2023)
5-140835338-C-T		not specified	Uncertain significance (Jul 11, 2023)
5-140835437-C-G		not specified	Likely benign (Aug 23, 2021)
5-140835485-G-T		not specified	Uncertain significance (Dec 06, 2022)
5-140835520-T-G		not specified	Uncertain significance (Oct 06, 2021)
5-140835530-G-C		not specified	Uncertain significance (Nov 14, 2023)
5-140835568-C-G		not specified	Uncertain significance (Dec 12, 2023)
5-140835571-G-T		not specified	Uncertain significance (Dec 17, 2021)
5-140835689-T-C		not specified	Uncertain significance (Oct 26, 2022)
5-140835767-G-A		not specified	Uncertain significance (Feb 28, 2023)
5-140835797-T-C			Likely benign (Mar 01, 2023)
5-140835798-G-C		not specified	Uncertain significance (Aug 02, 2023)
5-140835821-G-A		not specified	Likely benign (Jun 02, 2023)
5-140835878-G-T		not specified	Uncertain significance (Aug 30, 2022)
5-140835881-G-A		not specified	Uncertain significance (Dec 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHA7	protein_coding	protein_coding	ENST00000525929	4	177961

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.98e-9	0.836	125562	1	185	125748	0.000740

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.18	641	562	1.14	0.0000403	5986
Missense in Polyphen		132	121.31	1.0881		1411
Synonymous	-2.81	330	271	1.22	0.0000238	2042
Loss of Function	1.62	17	25.9	0.657	0.00000143	304

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000890	0.000889
Ashkenazi Jewish	0.000213	0.000198
East Asian	0.00415	0.00414
Finnish	0.00	0.00
European (Non-Finnish)	0.000344	0.000343
Middle Eastern	0.00415	0.00414
South Asian	0.00131	0.00131
Other	0.000822	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent cell-adhesion protein involved in cells self-recognition and non-self discrimination. Thereby, it is involved in the establishment and maintenance of specific neuronal connections in the brain. {ECO:0000250|UniProtKB:Q91Y13}.

Intolerance Scores

• loftool: 0.861
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.18

Haploinsufficiency Scores

• pHI: 0.0526
• hipred: N
• hipred_score: 0.305
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.111

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdha7

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;nervous system development;cell-cell recognition
• Cellular component: integral component of plasma membrane
• Molecular function: calcium ion binding;identical protein binding