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GeneBe

PDZD4

PDZ domain containing 4, the group of PDZ domain containing

Basic information

Region (hg38): X:153802165-153830565

Previous symbols: [ "PDZK4" ]

Links

ENSG00000067840NCBI:57595OMIM:300634HGNC:21167Uniprot:Q76G19AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDZD4 gene.

  • Inborn genetic diseases (25 variants)
  • not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDZD4 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
4
clinvar
4
missense
22
clinvar
4
clinvar
26
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 22 8 0

Variants in PDZD4

This is a list of pathogenic ClinVar variants found in the PDZD4 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-153803412-C-T Inborn genetic diseases Likely benign (Oct 06, 2021)2253817
X-153803467-C-T Likely benign (Dec 01, 2022)2661735
X-153803473-C-G Hand tremor;Kyphoscoliosis;Hypotonia;Autism;Abnormal facial shape Uncertain significance (Oct 09, 2022)1710148
X-153803643-G-A Inborn genetic diseases Uncertain significance (May 18, 2022)2290403
X-153803757-C-G Inborn genetic diseases Uncertain significance (Mar 17, 2023)2526122
X-153803869-G-C Inborn genetic diseases Uncertain significance (Jun 05, 2023)2557886
X-153804021-G-C Inborn genetic diseases Uncertain significance (May 16, 2023)2546758
X-153804024-G-A Inborn genetic diseases Uncertain significance (Jun 06, 2023)2557511
X-153804030-G-A Inborn genetic diseases Uncertain significance (Dec 07, 2021)2265503
X-153804082-G-C Inborn genetic diseases Uncertain significance (Dec 01, 2022)2382892
X-153804153-G-A Inborn genetic diseases Uncertain significance (May 13, 2022)2289627
X-153804158-A-C Inborn genetic diseases Uncertain significance (Jan 05, 2022)2270529
X-153804227-C-T Inborn genetic diseases Uncertain significance (Mar 24, 2023)2559098
X-153804253-G-A Likely benign (Feb 01, 2023)2661736
X-153804327-T-C Inborn genetic diseases Likely benign (Apr 07, 2023)2534428
X-153804332-G-C Inborn genetic diseases Likely benign (Apr 07, 2023)2567493
X-153804555-C-T Inborn genetic diseases Uncertain significance (Feb 10, 2022)2276445
X-153804590-C-G Inborn genetic diseases Uncertain significance (May 24, 2023)2551606
X-153804758-G-A Autism Uncertain significance (-)2579706
X-153804810-C-T Inborn genetic diseases Uncertain significance (Jul 28, 2021)2239852
X-153804837-G-C Inborn genetic diseases Uncertain significance (Jun 22, 2021)2381680
X-153805179-C-T Inborn genetic diseases Uncertain significance (Sep 26, 2022)2313433
X-153805183-C-T Inborn genetic diseases Uncertain significance (Feb 28, 2023)2490155
X-153806774-C-T Inborn genetic diseases Uncertain significance (Nov 15, 2021)2357422
X-153807302-G-A Inborn genetic diseases Uncertain significance (Jan 18, 2023)2472016

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PDZD4protein_codingprotein_codingENST00000164640 828400
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8490.151125594431256010.0000279
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.702393890.6140.00003934985
Missense in Polyphen70176.360.396921991
Synonymous0.4851651730.9530.00001791597
Loss of Function3.45319.40.1550.00000151310

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.0001350.0000993
East Asian0.00007220.0000544
Finnish0.000.00
European (Non-Finnish)0.00005030.0000352
Middle Eastern0.00007220.0000544
South Asian0.00005650.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.113

Intolerance Scores

loftool
0.121
rvis_EVS
-0.38
rvis_percentile_EVS
27.88

Haploinsufficiency Scores

pHI
0.468
hipred
Y
hipred_score
0.718
ghis
0.561

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.0335

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pdzd4
Phenotype
normal phenotype;

Gene ontology

Biological process
protein ubiquitination
Cellular component
cell cortex
Molecular function
ubiquitin protein ligase activity