PRDM15
Basic information
Region (hg38): 21:41798225-41879482
Previous symbols: [ "ZNF298", "C21orf83" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (199 variants)
- not_provided (12 variants)
- Pervasive_developmental_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDM15 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001040424.3. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 8 | |||||
missense | 139 | 144 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 1 | 139 | 12 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PRDM15 | protein_coding | protein_coding | ENST00000269844 | 31 | 81207 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000822 | 1.00 | 125699 | 0 | 49 | 125748 | 0.000195 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.42 | 703 | 908 | 0.774 | 0.0000597 | 9893 |
Missense in Polyphen | 171 | 304.74 | 0.56114 | 3035 | ||
Synonymous | 0.0933 | 385 | 387 | 0.994 | 0.0000297 | 2834 |
Loss of Function | 5.33 | 23 | 71.7 | 0.321 | 0.00000367 | 836 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000335 | 0.000333 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000272 | 0.000272 |
Finnish | 0.0000929 | 0.0000924 |
European (Non-Finnish) | 0.000214 | 0.000211 |
Middle Eastern | 0.000272 | 0.000272 |
South Asian | 0.000229 | 0.000229 |
Other | 0.000490 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Sequence-specific DNA-binding transcriptional regulator. Plays a role as a molecular node in a transcriptional network regulating embryonic development and cell fate decision. Stimulates the expression of upstream key transcriptional activators and repressors of the Wnt/beta-catenin and MAPK/ERK pathways, respectively, that are essential for naive pluripotency and self-renewal maintenance of embryonic stem cells (ESCs). Specifically promotes SPRY1 and RSPO1 transcription activation through recognition and direct binding of a specific DNA sequence in their promoter regions. Involved in early embryo development (By similarity). Plays also a role in induced pluripotent stem cells (iPSCs) reprogramming (PubMed:28740264). {ECO:0000250|UniProtKB:E9Q8T2, ECO:0000269|PubMed:28740264}.;
- Pathway
- FOXA1 transcription factor network;Validated nuclear estrogen receptor alpha network
(Consensus)
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- loftool
- 0.720
- rvis_EVS
- -2
- rvis_percentile_EVS
- 1.73
Haploinsufficiency Scores
- pHI
- 0.0747
- hipred
- N
- hipred_score
- 0.458
- ghis
- 0.626
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.143
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prdm15
- Phenotype
Gene ontology
- Biological process
- multicellular organism development;methylation;negative regulation of MAPK cascade;positive regulation of transcription by RNA polymerase II;positive regulation of canonical Wnt signaling pathway;regulation of stem cell division
- Cellular component
- nucleus;nucleoplasm;nuclear body
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;methyltransferase activity;metal ion binding;promoter-specific chromatin binding