PCDH11X

protocadherin 11 X-linked, the group of Non-clustered protocadherins|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): X:91779260-92623230

Previous symbols: [ "PCDH11" ]

Links

ENSG00000102290 ∙ NCBI:27328 ∙ OMIM:300246 ∙ HGNC:8656 ∙ Uniprot:Q9BZA7 ∙ 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 PCDH11X gene.

• Inborn genetic diseases (30 variants)
• not provided (22 variants)
• PCDH11X-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDH11X 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				6	5	11
missense			34	1	3	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	34	7	8

Variants in PCDH11X

This is a list of pathogenic ClinVar variants found in the PCDH11X region.

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

Position	Type	Phenotype	Significance	ClinVar
X-91835514-T-C			Benign (Dec 31, 2019)
X-91835516-G-T		not specified	Uncertain significance (Feb 15, 2023)
X-91835596-G-A			Uncertain significance (Aug 11, 2017)
X-91835742-G-A		not specified	Uncertain significance (May 05, 2023)
X-91835767-G-T		not specified	Uncertain significance (Oct 05, 2023)
X-91835776-T-C		not specified	Uncertain significance (Jan 18, 2022)
X-91835959-C-T		not specified	Uncertain significance (Apr 24, 2023)
X-91835977-A-G		not specified	Uncertain significance (May 24, 2023)
X-91876893-A-T		not specified	Uncertain significance (Mar 01, 2024)
X-91876958-A-T		not specified	Conflicting classifications of pathogenicity (Jan 02, 2024)
X-91877016-C-T		not specified	Uncertain significance (Oct 25, 2022)
X-91877043-T-G		not specified	Uncertain significance (Jul 05, 2023)
X-91877251-A-G			Likely benign (Mar 29, 2018)
X-91877524-C-T			Benign (Jun 01, 2018)
X-91877896-C-G			Uncertain significance (-)
X-91877897-A-G		not specified	Uncertain significance (Feb 15, 2023)
X-91877898-A-C		not specified	Uncertain significance (Dec 15, 2022)
X-91878090-C-A		not specified	Uncertain significance (Sep 01, 2021)
X-91878117-G-A		not specified	Uncertain significance (May 18, 2023)
X-91878198-G-A		not specified	Likely benign (Dec 28, 2022)
X-91878301-G-A			Benign (Dec 31, 2019)
X-91878335-A-C		not specified	Uncertain significance (Oct 27, 2021)
X-91878347-A-G		not specified	Uncertain significance (Dec 28, 2023)
X-91878392-G-A		not specified	Uncertain significance (Dec 21, 2023)
X-91878511-A-G			Likely benign (Mar 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDH11X	protein_coding	protein_coding	ENST00000373094	7	843970

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0158	0.984	125730	8	9	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	356	501	0.711	0.0000379	8878
Missense in Polyphen		88	195.52	0.45007		3799
Synonymous	-0.878	210	194	1.08	0.0000155	2750
Loss of Function	3.25	8	25.8	0.310	0.00000207	471

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000189	0.000160
Ashkenazi Jewish	0.000267	0.000198
East Asian	0.000216	0.000163
Finnish	0.0000625	0.0000462
European (Non-Finnish)	0.0000500	0.0000352
Middle Eastern	0.000216	0.000163
South Asian	0.000105	0.0000653
Other	0.000441	0.000326

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0851

Intolerance Scores

• loftool: 0.455
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.6

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.431
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.101

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdh11x

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;negative regulation of phosphatase activity
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: calcium ion binding