PDZD4
Basic information
Region (hg38): X:153802165-153830565
Previous symbols: [ "PDZK4" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 30 | 34 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 30 | 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 | not specified | Likely benign (Oct 06, 2021) | ||
X-153803467-C-T | Likely benign (Dec 01, 2022) | |||
X-153803473-C-G | Hand tremor;Autism;Hypotonia;Kyphoscoliosis;Abnormal facial shape | Uncertain significance (Oct 09, 2022) | ||
X-153803643-G-A | not specified | Uncertain significance (May 18, 2022) | ||
X-153803757-C-G | not specified | Uncertain significance (Mar 17, 2023) | ||
X-153803869-G-C | not specified | Uncertain significance (Jun 05, 2023) | ||
X-153803873-C-T | not specified | Uncertain significance (Mar 01, 2024) | ||
X-153804021-G-C | not specified | Uncertain significance (May 16, 2023) | ||
X-153804024-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
X-153804030-G-A | not specified | Uncertain significance (Dec 07, 2021) | ||
X-153804082-G-C | not specified | Uncertain significance (Dec 01, 2022) | ||
X-153804122-G-C | not specified | Uncertain significance (Nov 14, 2023) | ||
X-153804122-G-T | not specified | Likely benign (May 07, 2024) | ||
X-153804153-G-A | not specified | Uncertain significance (May 13, 2022) | ||
X-153804158-A-C | not specified | Uncertain significance (Jan 05, 2022) | ||
X-153804167-T-C | not specified | Uncertain significance (Feb 28, 2023) | ||
X-153804227-C-T | not specified | Uncertain significance (Mar 24, 2023) | ||
X-153804253-G-A | Likely benign (Feb 01, 2023) | |||
X-153804327-T-C | not specified | Likely benign (Apr 07, 2023) | ||
X-153804332-G-C | not specified | Likely benign (Apr 07, 2023) | ||
X-153804357-C-G | not specified | Uncertain significance (Jan 16, 2024) | ||
X-153804555-C-T | not specified | Uncertain significance (Feb 10, 2022) | ||
X-153804590-C-G | not specified | Uncertain significance (May 24, 2023) | ||
X-153804623-G-A | not specified | Uncertain significance (Mar 04, 2024) | ||
X-153804758-G-A | Autism | Uncertain significance (-) |
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