PRDM14
PR/SET domain 14, the group of PR/SET domain family|Zinc fingers C2H2-type
Basic information
Region (hg38): 8:70051651-70071693
Links
Phenotypes
GenCC
Source:
No genCC data.
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 PRDM14 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 | 21 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 21 | 0 | 0 |
Variants in PRDM14
This is a list of pathogenic ClinVar variants found in the PRDM14 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-70052132-A-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 8-70052237-C-T | not specified | Uncertain significance (Aug 16, 2022) | ||
| 8-70055305-T-C | not specified | Uncertain significance (Mar 25, 2024) | ||
| 8-70058696-G-A | not specified | Uncertain significance (May 03, 2023) | ||
| 8-70066264-G-A | not specified | Uncertain significance (Dec 08, 2023) | ||
| 8-70068337-A-G | not specified | Uncertain significance (Apr 04, 2023) | ||
| 8-70068361-C-T | not specified | Uncertain significance (Sep 25, 2023) | ||
| 8-70068367-C-A | not specified | Uncertain significance (Nov 07, 2022) | ||
| 8-70068369-G-A | not specified | Uncertain significance (Oct 29, 2021) | ||
| 8-70069248-C-T | not specified | Uncertain significance (Nov 02, 2023) | ||
| 8-70069333-C-G | not specified | Uncertain significance (Oct 03, 2022) | ||
| 8-70069446-C-T | not specified | Uncertain significance (Jan 09, 2023) | ||
| 8-70069508-C-G | not specified | Uncertain significance (Nov 09, 2021) | ||
| 8-70069570-C-A | not specified | Uncertain significance (Sep 22, 2023) | ||
| 8-70069584-G-A | not specified | Uncertain significance (Aug 15, 2023) | ||
| 8-70069647-G-A | not specified | Uncertain significance (Jan 26, 2022) | ||
| 8-70069653-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
| 8-70069659-G-A | not specified | Uncertain significance (Oct 18, 2021) | ||
| 8-70069671-G-A | not specified | Uncertain significance (Sep 07, 2022) | ||
| 8-70069680-A-C | not specified | Uncertain significance (Feb 05, 2024) | ||
| 8-70069700-C-T | not specified | Uncertain significance (Jan 20, 2023) | ||
| 8-70069703-A-C | not specified | Uncertain significance (Apr 23, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PRDM14 | protein_coding | protein_coding | ENST00000276594 | 7 | 20043 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0194 | 0.980 | 125731 | 0 | 17 | 125748 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.88 | 226 | 321 | 0.704 | 0.0000166 | 3742 |
| Missense in Polyphen | 46 | 111.53 | 0.41244 | 1310 | ||
| Synonymous | 1.18 | 111 | 128 | 0.867 | 0.00000658 | 1095 |
| Loss of Function | 2.95 | 7 | 21.9 | 0.319 | 0.00000111 | 264 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000867 | 0.0000867 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000235 | 0.000231 |
| European (Non-Finnish) | 0.0000355 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000181 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor that has both positive and negative roles on transcription. Required for the maintenance of emryonic stem cell identity and the reacquisition of pluripotency in somatic cells. May play an essential role in germ cell development at 2 levels: the reacquisition of potential pluripotency, including SOX2 up-regulation, and successful epigenetic reprogramming, characterized by EHMT1 repression. Its association with CBFA2T2 is required for the functions in pluripotency and germ cell formation (By similarity). Directly up-regulates the expression of pluripotency gene POU5F1 through its proximal enhancer. Binds to the DNA consensus sequence 5'-GGTC[TC]CTAA-3'. {ECO:0000250|UniProtKB:E9Q3T6, ECO:0000269|PubMed:17942894, ECO:0000269|PubMed:20953172}.;
- Pathway
- Endoderm Differentiation;Developmental Biology;Transcriptional regulation of pluripotent stem cells
(Consensus)
Recessive Scores
- pRec
- 0.101
Intolerance Scores
- loftool
- 0.431
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.45
Haploinsufficiency Scores
- pHI
- 0.393
- hipred
- Y
- hipred_score
- 0.568
- ghis
- 0.420
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prdm14
- Phenotype
- growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; hearing/vestibular/ear phenotype; vision/eye phenotype;
Zebrafish Information Network
- Gene name
- prdm14
- Affected structure
- CaP motoneuron
- Phenotype tag
- abnormal
- Phenotype quality
- decreased length
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;cell morphogenesis;cell fate specification;inner cell mass cell fate commitment;germ cell development;embryo implantation;fertilization;germ-line stem cell population maintenance;histone H3-R26 methylation;somatic stem cell population maintenance;negative regulation of fibroblast growth factor receptor signaling pathway;regulation of DNA methylation;homeostasis of number of cells within a tissue;inactivation of paternal X chromosome;positive regulation of flagellated sperm motility;positive regulation of stem cell population maintenance
- Cellular component
- nucleus;nucleoplasm
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;RNA binding;protein binding;methyltransferase activity;chromatin DNA binding;sequence-specific DNA binding;metal ion binding