PDZD11

PDZ domain containing 11, the group of PDZ domain containing

Basic information

Region (hg38): X:70281117-70290514

Previous symbols: [ "PDZK11" ]

Links

ENSG00000120509 ∙ NCBI:51248 ∙ OMIM:300632 ∙ HGNC:28034 ∙ Uniprot:Q5EBL8 ∙ 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 PDZD11 gene.

• not provided (4 variants)
• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDZD11 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						0
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	3	1	7
Total	0	0	4	3	1

Variants in PDZD11

This is a list of pathogenic ClinVar variants found in the PDZD11 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-70281705-C-T		Inborn genetic diseases	Uncertain significance (May 26, 2022)
X-70282242-G-C		not specified	Uncertain significance (Oct 27, 2023)
X-70282339-G-A		not specified	Uncertain significance (Feb 13, 2024)
X-70282348-G-A			Likely benign (Feb 01, 2023)
X-70282563-T-C		not specified	Uncertain significance (Dec 02, 2022)
X-70282837-G-A		not specified	Uncertain significance (Sep 30, 2021)
X-70283304-C-T		not specified	Uncertain significance (Dec 01, 2022)
X-70283553-C-T			Likely benign (May 01, 2023)
X-70284588-CG-C			Benign (May 03, 2018)
X-70284614-G-C		not specified	Uncertain significance (May 17, 2023)
X-70284647-C-T			Likely benign (Jan 01, 2023)
X-70287311-C-T		not specified	Uncertain significance (Aug 16, 2022)
X-70287312-G-A		not specified	Uncertain significance (Aug 21, 2023)
X-70290433-C-T			Likely benign (-)
X-70290485-C-T		Intellectual disability, X-linked 100	Benign (Aug 19, 2021)
X-70290485-C-C			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDZD11	protein_coding	protein_coding	ENST00000239666	6	3920

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.199	0.761	125697	1	1	125699	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.75	19	55.8	0.340	0.00000442	920
Missense in Polyphen		3	10.734	0.27948		210
Synonymous	0.237	17	18.3	0.929	0.00000130	264
Loss of Function	1.70	2	6.78	0.295	5.76e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000723	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000723	0.0000544
South Asian	0.00	0.00
Other	0.000221	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Ion influx/efflux at host-pathogen interface;Biotin transport and metabolism;Ion channel transport;Antimicrobial peptides;Innate Immune System;Immune System;Metabolism;Vitamin B5 (pantothenate) metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;EGFR1;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.96

Haploinsufficiency Scores

• pHI: 0.0977
• hipred: Y
• hipred_score: 0.592
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdzd11

Gene ontology

• Biological process: neurotransmitter secretion;maintenance of epithelial cell apical/basal polarity;protein localization to basolateral plasma membrane
• Cellular component: extracellular region;cytosol;cell-cell junction;basolateral plasma membrane;synapse;presynapse
• Molecular function: protein binding