PDZD2

PDZ domain containing 2, the group of PDZ domain containing

Basic information

Region (hg38): 5:31639131-32110932

Previous symbols: [ "PDZK3" ]

Links

ENSG00000133401NCBI:23037OMIM:610697HGNC:18486Uniprot:O15018AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDZD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDZD2 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
34
clinvar
22
clinvar
56
missense
166
clinvar
29
clinvar
22
clinvar
217
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
1
clinvar
1
Total 0 0 167 63 46

Variants in PDZD2

This is a list of pathogenic ClinVar variants found in the PDZD2 region.

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

Position Type Phenotype Significance ClinVar
5-31799264-G-A PDZD2-related disorder Benign (Dec 31, 2019)776038
5-31799331-A-T not specified Uncertain significance (Oct 14, 2023)3211164
5-31799337-C-G Benign (Aug 08, 2018)745813
5-31799359-G-A PDZD2-related disorder Benign (May 31, 2019)3041665
5-31799372-C-A not specified Uncertain significance (Dec 19, 2023)3211118
5-31799415-C-T PDZD2-related disorder Benign (Feb 24, 2020)3037252
5-31799440-C-T PDZD2-related disorder Benign (Nov 18, 2019)3049244
5-31799519-C-T not specified Uncertain significance (Dec 21, 2022)2338404
5-31799528-G-A not specified Uncertain significance (Nov 07, 2024)3416722
5-31799528-G-C not specified Uncertain significance (Apr 08, 2024)3305646
5-31799540-G-A not specified Uncertain significance (Oct 04, 2022)2316104
5-31799547-G-T not specified Uncertain significance (Jun 22, 2021)2321206
5-31799585-G-A not specified Uncertain significance (Nov 25, 2024)3416763
5-31799618-C-A not specified Uncertain significance (Oct 08, 2024)3416754
5-31799663-C-T not specified Uncertain significance (Dec 21, 2022)2395522
5-31799664-G-A not specified Uncertain significance (Jul 14, 2021)2394400
5-31799699-G-A not specified Uncertain significance (Jun 22, 2024)3305655
5-31983157-A-T PDZD2-related disorder Likely benign (May 02, 2019)3053793
5-31983211-G-A not specified Uncertain significance (Apr 25, 2022)2286151
5-31983234-A-T not specified Uncertain significance (Dec 02, 2024)3416765
5-31983245-C-T PDZD2-related disorder Likely benign (Oct 26, 2023)2637315
5-31983255-A-T not specified Uncertain significance (Dec 20, 2022)2359054
5-31983280-C-T not specified Uncertain significance (Aug 26, 2024)3416724
5-31983301-G-A not specified Likely benign (Jan 31, 2024)3211147
5-31983310-A-G not specified Uncertain significance (Nov 24, 2024)3416727

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PDZD2protein_codingprotein_codingENST00000438447 24471521
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9970.003061256501971257480.000390
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.6914391.63e+30.8820.000096818372
Missense in Polyphen404544.80.741556266
Synonymous-0.2326936851.010.00004456023
Loss of Function7.55191010.1880.000005661210

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001380.00138
Ashkenazi Jewish0.00009920.0000992
East Asian0.0002220.000217
Finnish0.0001850.000185
European (Non-Finnish)0.0003270.000308
Middle Eastern0.0002220.000217
South Asian0.0003940.000359
Other0.0001680.000163

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.162

Intolerance Scores

loftool
0.533
rvis_EVS
0.25
rvis_percentile_EVS
69.67

Haploinsufficiency Scores

pHI
0.115
hipred
N
hipred_score
0.321
ghis
0.486

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.581

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pdzd2
Phenotype

Gene ontology

Biological process
cell adhesion
Cellular component
extracellular region;nucleus;cytoplasm;endoplasmic reticulum;cell-cell junction
Molecular function