PDZD4
PDZ domain containing 4, the group of PDZ domain containing
Basic information
Region (hg38): X:153802165-153830565
Previous symbols: [ "PDZK4" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- 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) | ||
X-153803473-C-G | Hand tremor;Kyphoscoliosis;Hypotonia;Autism;Abnormal facial shape | Uncertain significance (Oct 09, 2022) | ||
X-153803643-G-A | Inborn genetic diseases | Uncertain significance (May 18, 2022) | ||
X-153803757-C-G | Inborn genetic diseases | Uncertain significance (Mar 17, 2023) | ||
X-153803869-G-C | Inborn genetic diseases | Uncertain significance (Jun 05, 2023) | ||
X-153804021-G-C | Inborn genetic diseases | Uncertain significance (May 16, 2023) | ||
X-153804024-G-A | Inborn genetic diseases | Uncertain significance (Jun 06, 2023) | ||
X-153804030-G-A | Inborn genetic diseases | Uncertain significance (Dec 07, 2021) | ||
X-153804082-G-C | Inborn genetic diseases | Uncertain significance (Dec 01, 2022) | ||
X-153804153-G-A | Inborn genetic diseases | Uncertain significance (May 13, 2022) | ||
X-153804158-A-C | Inborn genetic diseases | Uncertain significance (Jan 05, 2022) | ||
X-153804227-C-T | Inborn genetic diseases | Uncertain significance (Mar 24, 2023) | ||
X-153804327-T-C | Inborn genetic diseases | Likely benign (Apr 07, 2023) | ||
X-153804332-G-C | Inborn genetic diseases | Likely benign (Apr 07, 2023) | ||
X-153804555-C-T | Inborn genetic diseases | Uncertain significance (Feb 10, 2022) | ||
X-153804590-C-G | Inborn genetic diseases | Uncertain significance (May 24, 2023) | ||
X-153804758-G-A | Autism | Uncertain significance (-) | ||
X-153804810-C-T | Inborn genetic diseases | Uncertain significance (Jul 28, 2021) | ||
X-153804837-G-C | Inborn genetic diseases | Uncertain significance (Jun 22, 2021) | ||
X-153805179-C-T | Inborn genetic diseases | Uncertain significance (Sep 26, 2022) | ||
X-153805183-C-T | Inborn genetic diseases | Uncertain significance (Feb 28, 2023) | ||
X-153806774-C-T | Inborn genetic diseases | Uncertain significance (Nov 15, 2021) | ||
X-153807302-G-A | Inborn genetic diseases | Uncertain significance (Jan 18, 2023) | ||
X-153807337-G-T | Inborn genetic diseases | Uncertain significance (Aug 16, 2022) | ||
X-153807340-G-A | Inborn genetic diseases | Uncertain significance (Jul 14, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PDZD4 | protein_coding | protein_coding | ENST00000164640 | 8 | 28400 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.849 | 0.151 | 125594 | 4 | 3 | 125601 | 0.0000279 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.70 | 239 | 389 | 0.614 | 0.0000393 | 4985 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.000135 | 0.0000993 |
East Asian | 0.0000722 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000503 | 0.0000352 |
Middle Eastern | 0.0000722 | 0.0000544 |
South Asian | 0.0000565 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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