PCDH11Y

protocadherin 11 Y-linked, the group of Non-clustered protocadherins

Basic information

Region (hg38): Y:5000226-5742224

Previous symbols: [ "PCDH22" ]

Links

ENSG00000099715 ∙ NCBI:83259 ∙ OMIM:400022 ∙ HGNC:15813 ∙ Uniprot:Q9BZA8 ∙ 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 PCDH11Y gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDH11Y 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in PCDH11Y

This is a list of pathogenic ClinVar variants found in the PCDH11Y region.

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

Position	Type	Phenotype	Significance	ClinVar
Y-5100116-G-T			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDH11Y	protein_coding	protein_coding	ENST00000362095	3	741999

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000168	0.466	67921	30	0	67951	0.000221

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.140	175	170	1.03	0.0000264	6940
Missense in Polyphen		57	62.075	0.91824		2843
Synonymous	0.876	58	67.1	0.864	0.0000111	2146
Loss of Function	0.289	6	6.81	0.881	0.00000111	335

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00103	0.000863
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000110
Finnish	0.000177	0.0000887
European (Non-Finnish)	0.000517	0.000252
Middle Eastern	0.000223	0.000110
South Asian	0.000434	0.000217
Other	0.000624	0.000311

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0839

Haploinsufficiency Scores

• pHI: 0.0723
• hipred: N
• hipred_score: 0.112
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0421

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