PDZD2

protein-coding

PDZ domain containing 2, the group of PDZ domain containing

Gene summary

The protein encoded by this gene contains six PDZ domains and shares sequence similarity with pro-interleukin-16 (pro-IL-16). Like pro-IL-16, the encoded protein localizes to the endoplasmic reticulum and is thought to be cleaved by a caspase to produce a secreted peptide containing two PDZ domains. In addition, this gene is upregulated in primary prostate tumors and may be involved in the early stages of prostate tumorigenesis. [provided by RefSeq, Dec 2015]

Previous symbols:

PDZK3

MANE transcript

NM_178140.4

Inheritance

—

ClinVar variants

U:445B:120

Top phenotype

PDZD2-related disorder

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr5:31,639,131-32,110,932

External References & Databases

Ensembl (ENSG00000133401)

Transcript & Mutation Effects

hg38 • Region Span ~471.8 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 PDZD2 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 459

PDZD2-related disorderTotal: 83

not providedTotal: 27

LissencephalyTotal: 1

ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178140.4. 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			6 clinvar	39 clinvar	16 clinvar	61
missense			429 clinvar	49 clinvar	16 clinvar	494
nonsense			3 clinvar			3
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	445	88	32	565

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178140.4	RefSeq	NP_835260.2	24	MANE Select
ENST00000438447.2	Ensembl	ENSP00000402033.1	24	MANE Select
ENST00000513910.1	Ensembl	ENSP00000424901.1	1	Standard
ENST00000942338.1	Ensembl	ENSP00000612397.1	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell adhesion

Cellular Component

extracellular region
nucleus
cytoplasm
endoplasmic reticulum
cell-cell junction

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000438447
Coding exons: 24
Length: 471521
Individuals with no LoFs: 125650
Homozygous LoFs: 1
Heterozygous LoFs: 97
Defined: 125748
p: 0.000390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.69	1439	1.63e+3	0.882	0.0000968	18372
Missense (PolyPhen)		404	544.8	0.74155		6266
Synonymous	-0.232	693	685	1.01	0.0000445	6023
Loss of Function	7.55	19	101	0.188	0.00000566	1210

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00033	0.00031	rare
South Asian	0.00039	0.00036	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.162

Intolerance Scores

LoFtool: 0.533
RVIS EVS: 0.25
RVIS percentile EVS: 69.67

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.581

Gene Damage Prediction

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