PCDH18

protocadherin 18, the group of Non-clustered protocadherins

Basic information

Region (hg38): 4:137518918-137532494

Links

ENSG00000189184 ∙ NCBI:54510 ∙ OMIM:608287 ∙ HGNC:14268 ∙ Uniprot:Q9HCL0 ∙ 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 PCDH18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDH18 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				1		1
missense			78	2		80
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	80	3	0

Variants in PCDH18

This is a list of pathogenic ClinVar variants found in the PCDH18 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-137521076-G-C		not specified	Uncertain significance (Apr 04, 2023)
4-137521078-T-C		not specified	Uncertain significance (Apr 26, 2023)
4-137521101-T-A		not specified	Uncertain significance (Dec 14, 2021)
4-137521108-T-C		not specified	Uncertain significance (Mar 21, 2023)
4-137521111-T-C		not specified	Uncertain significance (Jan 24, 2025)
4-137521220-G-A		not specified	Uncertain significance (Oct 29, 2021)
4-137521221-T-C			Likely benign (Jan 01, 2023)
4-137521223-G-A		not specified	Uncertain significance (Jul 09, 2021)
4-137521274-C-A		not specified	Uncertain significance (Mar 16, 2024)
4-137521276-G-A		not specified	Uncertain significance (Dec 21, 2022)
4-137521283-C-G		not specified	Uncertain significance (Aug 13, 2021)
4-137521294-C-G		not specified	Uncertain significance (Jun 16, 2023)
4-137521294-C-T		not specified	Uncertain significance (Mar 16, 2022)
4-137521295-C-A		not specified	Uncertain significance (Nov 02, 2023)
4-137521303-T-C		not specified	Uncertain significance (Mar 01, 2025)
4-137521336-G-T		not specified	Uncertain significance (May 15, 2024)
4-137521339-T-C		not specified	Uncertain significance (Sep 25, 2023)
4-137521413-C-T		not specified	Uncertain significance (Jul 26, 2022)
4-137521571-T-C		not specified	Likely benign (Feb 27, 2023)
4-137521586-C-A		not specified	Uncertain significance (May 05, 2022)
4-137521613-C-T		not specified	Uncertain significance (Dec 03, 2024)
4-137521630-A-G		not specified	Uncertain significance (Apr 13, 2023)
4-137528509-G-T		not specified	Uncertain significance (Dec 12, 2023)
4-137528522-T-G		not specified	Uncertain significance (Aug 01, 2022)
4-137528552-C-T		not specified	Uncertain significance (Nov 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDH18	protein_coding	protein_coding	ENST00000344876	4	13577

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.127	0.873	125664	0	23	125687	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.629	563	607	0.928	0.0000301	7498
Missense in Polyphen		192	239.15	0.80284		3007
Synonymous	-0.952	250	232	1.08	0.0000124	2251
Loss of Function	3.90	8	31.7	0.253	0.00000169	416

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000330	0.000329
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000708	0.0000704
Middle Eastern	0.000109	0.000109
South Asian	0.0000655	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential calcium-dependent cell-adhesion protein.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.514
• rvis_EVS: -1.26
• rvis_percentile_EVS: 5.31

Haploinsufficiency Scores

• pHI: 0.180
• hipred: Y
• hipred_score: 0.544
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.287

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdh18
• Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; skeleton phenotype; vision/eye phenotype; limbs/digits/tail phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: pcdh18b
• Affected structure: primary motor neuron
• Phenotype tag: abnormal
• Phenotype quality: has fewer parts of type

Gene ontology

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