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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:Q76G19AlphaFoldGenCCjaxSfariGnomADPubmed

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 (15 variants)
  • Movement disorder;Coarse facial features;Microcephaly;Hyperactivity;Intellectual disability (1 variants)
  • Hypotonia;Autism;Hand tremor;Abnormal facial shape;Kyphoscoliosis (1 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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 0
missense 15 1 16
nonsense 0
start loss 0
frameshift 1 1
inframe indel 0
splice variant 0
non coding 0
Total 0 0 16 1 0

Variants in PDZD4

This is a list of pathogenic ClinVar variants found in the PDZD4 region.

Position Type Phenotype Significance ClinVar
X-153803412-C-T Inborn genetic diseases Likely benign (Oct 06, 2021)link
X-153803473-C-G Hand tremor;Kyphoscoliosis;Hypotonia;Autism;Abnormal facial shape Uncertain significance (Oct 09, 2022)link
X-153803643-G-A Inborn genetic diseases Uncertain significance (May 18, 2022)link
X-153803757-C-G Inborn genetic diseases Uncertain significance (Mar 17, 2023)link
X-153803869-G-C Inborn genetic diseases Uncertain significance (Jun 05, 2023)link
X-153804021-G-C Inborn genetic diseases Uncertain significance (May 16, 2023)link
X-153804024-G-A Inborn genetic diseases Uncertain significance (Jun 06, 2023)link
X-153804030-G-A Inborn genetic diseases Uncertain significance (Dec 07, 2021)link
X-153804082-G-C Inborn genetic diseases Uncertain significance (Dec 01, 2022)link
X-153804153-G-A Inborn genetic diseases Uncertain significance (May 13, 2022)link
X-153804158-A-C Inborn genetic diseases Uncertain significance (Jan 05, 2022)link
X-153804227-C-T Inborn genetic diseases Uncertain significance (Mar 24, 2023)link
X-153804327-T-C Inborn genetic diseases Likely benign (Apr 07, 2023)link
X-153804332-G-C Inborn genetic diseases Likely benign (Apr 07, 2023)link
X-153804555-C-T Inborn genetic diseases Uncertain significance (Feb 10, 2022)link
X-153804590-C-G Inborn genetic diseases Uncertain significance (May 24, 2023)link
X-153804758-G-A Autism Uncertain significance (-)link
X-153804810-C-T Inborn genetic diseases Uncertain significance (Jul 28, 2021)link
X-153804837-G-C Inborn genetic diseases Uncertain significance (Jun 22, 2021)link
X-153805179-C-T Inborn genetic diseases Uncertain significance (Sep 26, 2022)link
X-153805183-C-T Inborn genetic diseases Uncertain significance (Feb 28, 2023)link
X-153806774-C-T Inborn genetic diseases Uncertain significance (Nov 15, 2021)link
X-153807302-G-A Inborn genetic diseases Uncertain significance (Jan 18, 2023)link
X-153807337-G-T Inborn genetic diseases Uncertain significance (Aug 16, 2022)link
X-153807340-G-A Inborn genetic diseases Uncertain significance (Jul 14, 2021)link

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