PDZD4

protein-coding

PDZ domain containing 4, the group of PDZ domain containing

Gene summary

Predicted to be located in cell cortex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

PDZK4

MANE transcript

NM_001303512.2

Inheritance

—

ClinVar variants

U:103B:9

Top phenotype

Autism

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chrX:153,802,166-153,830,565

External References & Databases

Ensembl (ENSG00000067840)

Transcript & Mutation Effects

hg38 • Region Span ~28.4 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 PDZD4 variants in ClinVar

12 Conditions Cataloged

not specifiedTotal: 83

not providedTotal: 5

AutismTotal: 2

Hand tremorTotal: 1

HypotoniaTotal: 1

HyperactivityTotal: 1

Coarse facial featuresTotal: 1

Abnormal facial shapeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001303512.2. 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			7 clinvar	4 clinvar		11
missense			91 clinvar	5 clinvar		96
nonsense			3 clinvar			3
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	103	9	0	112

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001303512.2	RefSeq	NP_001290441.1	8	MANE Select
ENST00000393758.7	Ensembl	ENSP00000377355.3	8	MANE Select
NM_001303513.3	RefSeq	NP_001290442.1	7	Standard
NM_001303514.2	RefSeq	NP_001290443.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein ubiquitination

Molecular Function

ubiquitin protein ligase activity

Cellular Component

cell cortex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000164640
Coding exons: 8
Length: 28400
Individuals with no LoFs: 125594
Homozygous LoFs: 4
Heterozygous LoFs: 3
Defined: 125601
p: 0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.70	239	389	0.614	0.0000393	4985
Missense (PolyPhen)		70	176.36	0.39692		1991
Synonymous	0.485	165	173	0.953	0.0000179	1597
Loss of Function	3.45	3	19.4	0.155	0.00000151	310

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00013	0.000099	rare
East Asian	0.000072	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000050	0.000035	rare
South Asian	0.000056	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.121
RVIS EVS: -0.38
RVIS percentile EVS: 27.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0335

Gene Damage Prediction

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