DPPA4
Basic information
Region (hg38): 3:109326144-109337546
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 DPPA4 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 | 0 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 0 |
Variants in DPPA4
This is a list of pathogenic ClinVar variants found in the DPPA4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-109327996-A-G | Malignant tumor of prostate | Uncertain significance (-) | ||
| 3-109328984-C-T | not specified | Uncertain significance (Nov 11, 2024) | ||
| 3-109330536-G-T | not specified | Uncertain significance (Aug 04, 2024) | ||
| 3-109330602-C-G | not specified | Uncertain significance (Nov 12, 2024) | ||
| 3-109330788-C-T | not specified | Uncertain significance (Jul 16, 2024) | ||
| 3-109331927-G-T | not specified | Uncertain significance (Oct 17, 2023) | ||
| 3-109337513-A-C | not specified | Uncertain significance (Nov 14, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DPPA4 | protein_coding | protein_coding | ENST00000335658 | 7 | 11432 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000294 | 0.945 | 125734 | 0 | 12 | 125746 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.343 | 150 | 162 | 0.924 | 0.00000815 | 1964 |
| Missense in Polyphen | 26 | 44.877 | 0.57936 | 563 | ||
| Synonymous | -1.54 | 77 | 61.7 | 1.25 | 0.00000314 | 604 |
| Loss of Function | 1.72 | 8 | 15.2 | 0.525 | 6.89e-7 | 182 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000904 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.0000528 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in the maintenance of active epigenetic status of target genes. May inhibit differentiation of embryonic cells into a primitive ectoderm lineage. {ECO:0000250|UniProtKB:Q8CCG4}.;
- Pathway
- POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation;Developmental Biology;POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation;Transcriptional regulation of pluripotent stem cells
(Consensus)
Recessive Scores
- pRec
- 0.0620
Intolerance Scores
- loftool
- 0.679
- rvis_EVS
- 0.1
- rvis_percentile_EVS
- 61.49
Haploinsufficiency Scores
- pHI
- 0.363
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.401
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.213
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dppa4
- Phenotype
- growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; respiratory system phenotype; skeleton phenotype;
Gene ontology
- Biological process
- multicellular organism development;somatic stem cell population maintenance
- Cellular component
- nucleoplasm
- Molecular function
- chromatin binding;protein binding