PCDH11Y

protein-coding

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

Gene summary

This gene belongs to the protocadherin family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing seven cadherin repeats, a transmembrane domain, and a cytoplasmic tail that differs from those of the classical cadherins. This gene is located on the Y chromosome in a block of X/Y homology and is very closely related to its paralog on the X chromosome. The protein is thought to play a role in cell-cell recognition during development of the central nervous system. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

Previous symbols:

PCDH22

MANE transcript

NM_001395587.1

Inheritance

—

ClinVar variants

U:6B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chrY:5,000,226-5,742,224

External References & Databases

Ensembl (ENSG00000099715)

Transcript & Mutation Effects

hg38 • Region Span ~742.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PCDH11Y variants in ClinVar

1 Conditions Cataloged

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001395587.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	1 clinvar		4
missense			2 clinvar			2
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	6	1	0	7

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001395587.1	RefSeq	NP_001382516.1	5	MANE Select
ENST00000698851.1	Ensembl	ENSP00000513983.1	5	MANE Select
NM_001278619.2	RefSeq	NP_001265548.1	4	Standard
NM_032971.3	RefSeq	NP_116753.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell adhesion
homophilic cell adhesion via plasma membrane adhesion molecules

Molecular Function

calcium ion binding

Cellular Component

integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000362095
Coding exons: 3
Length: 741999
Individuals with no LoFs: 67921
Homozygous LoFs: 30
Heterozygous LoFs: 0
Defined: 67951
p: 0.000221

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.140	175	170	1.03	0.0000264	6940
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00032	0.00016	rare
Latino/Admixed American	0.00070	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00011	rare
Finnish	0.00018	0.000089	rare
European (Non-Finnish)	0.00052	0.00025	rare
South Asian	0.00043	0.00022	rare
Other	0.00062	0.00031	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0839

Essentials

Essential (CRISPR): N
Indispensability pred.: N
Indispensability score: 0.0421