PCDHA11

protocadherin alpha 11, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140868182-141012347

Previous symbols: [ "CNRS7" ]

Links

ENSG00000249158 ∙ NCBI:56138 ∙ OMIM:606317 ∙ HGNC:8665 ∙ Uniprot:Q9Y5I1 ∙ 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 PCDHA11 gene.

• Inborn genetic diseases (214 variants)
• not provided (23 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHA11 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		6
missense			41	9		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			158	23		181
Total	0	0	199	38	0

Variants in PCDHA11

This is a list of pathogenic ClinVar variants found in the PCDHA11 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140869201-A-G			Likely benign (Sep 01, 2022)
5-140869261-G-A		not specified	Uncertain significance (Dec 28, 2022)
5-140869285-A-C			Likely benign (Mar 01, 2023)
5-140869396-A-G		not specified	Likely benign (Dec 20, 2023)
5-140869410-A-G		not specified	Uncertain significance (Nov 17, 2023)
5-140869461-A-G		not specified	Likely benign (May 08, 2023)
5-140869497-G-A		not specified	Uncertain significance (May 11, 2022)
5-140869590-G-A		not specified	Uncertain significance (Dec 13, 2022)
5-140869617-C-G		not specified	Uncertain significance (Jan 29, 2024)
5-140869619-A-G			Likely benign (Sep 01, 2022)
5-140869756-G-A		not specified	Uncertain significance (Jun 28, 2023)
5-140869783-G-C		not specified	Uncertain significance (Dec 02, 2021)
5-140869826-G-T		not specified	Uncertain significance (Mar 01, 2024)
5-140869927-G-A		not specified	Uncertain significance (Nov 22, 2023)
5-140870020-C-T		not specified	Likely benign (Sep 14, 2022)
5-140870037-A-G		not specified	Uncertain significance (Oct 05, 2021)
5-140870071-A-G		not specified	Uncertain significance (Apr 07, 2023)
5-140870085-C-T		not specified	Uncertain significance (Mar 29, 2023)
5-140870098-A-G		not specified	Uncertain significance (Aug 14, 2023)
5-140870099-C-A		not specified	Uncertain significance (May 27, 2022)
5-140870217-A-G		not specified	Uncertain significance (Feb 06, 2023)
5-140870269-C-T		not specified	Uncertain significance (Dec 06, 2021)
5-140870317-C-G		not specified	Uncertain significance (Aug 14, 2023)
5-140870352-G-T		not specified	Uncertain significance (Dec 08, 2023)
5-140870364-G-A		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHA11	protein_coding	protein_coding	ENST00000398640	4	143241

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.46e-17	0.0475	125509	0	239	125748	0.000951

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.624	627	585	1.07	0.0000408	6068
Missense in Polyphen		175	166.88	1.0487		1870
Synonymous	-1.02	310	288	1.08	0.0000245	2054
Loss of Function	0.812	28	33.0	0.848	0.00000184	359

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00126	0.00123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000653	0.000653
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000304	0.000299
Middle Eastern	0.000653	0.000653
South Asian	0.00523	0.00517
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Intolerance Scores

• loftool: 0.834
• rvis_EVS: 1.08
• rvis_percentile_EVS: 91.76

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.172
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcdha11

Gene ontology

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