PDZD11

protein-coding

PDZ domain containing 11, the group of PDZ domain containing

Gene summary

Predicted to enable protein-macromolecule adaptor activity. Involved in pore complex assembly. Located in basolateral plasma membrane and cytosol. Part of pore complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

PDZK11

MANE transcript

NM_016484.5

Inheritance

—

ClinVar variants

U:33

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chrX:70,281,118-70,290,514

External References & Databases

Ensembl (ENSG00000120509)

Transcript & Mutation Effects

hg38 • Region Span ~9.4 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 PDZD11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 8

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016484.5. 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			3
missense			16 clinvar			16
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			13 clinvar			13
Total	0	0	33	0	0	33

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 61 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016484.5	RefSeq	NP_057568.1	6	MANE Select
ENST00000239666.9	Ensembl	ENSP00000239666.4	6	MANE Select
NM_001370174.1	RefSeq	NP_001357103.1	6	Standard
NM_001370175.1	RefSeq	NP_001357104.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ion influx/efflux at host-pathogen interface
Biotin transport and metabolism
Ion channel transport
Antimicrobial peptides
Innate Immune System

Biological Process

neurotransmitter secretion
maintenance of epithelial cell apical/basal polarity
protein localization to basolateral plasma membrane

Molecular Function

protein binding

Cellular Component

extracellular region
cytosol
cell-cell junction
basolateral plasma membrane
synapse

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000239666
Coding exons: 6
Length: 3920
Individuals with no LoFs: 125697
Homozygous LoFs: 1
Heterozygous LoFs: 1
Defined: 125699
p: 0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.75	19	55.8	0.340	0.00000442	920
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000072	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0.00022	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.109

Intolerance Scores

RVIS EVS: 0.1
RVIS percentile EVS: 60.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.508

Gene Damage Prediction

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