PHF19
PHD finger protein 19, the group of PHD finger proteins|Tudor domain containing
Basic information
Region (hg38): 9:120855651-120894896
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 PHF19 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 | 19 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 19 | 0 | 0 |
Variants in PHF19
This is a list of pathogenic ClinVar variants found in the PHF19 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-120858025-C-G | not specified | Uncertain significance (Nov 14, 2023) | ||
| 9-120858047-C-T | not specified | Uncertain significance (Oct 27, 2023) | ||
| 9-120858240-T-A | not specified | Uncertain significance (Oct 05, 2023) | ||
| 9-120862609-T-C | not specified | Uncertain significance (May 27, 2022) | ||
| 9-120862612-C-T | not specified | Uncertain significance (Dec 28, 2023) | ||
| 9-120862697-T-C | not specified | Uncertain significance (Jul 05, 2023) | ||
| 9-120862716-C-G | not specified | Uncertain significance (Jun 07, 2023) | ||
| 9-120862728-G-C | not specified | Uncertain significance (Oct 02, 2023) | ||
| 9-120865766-A-G | not specified | Uncertain significance (Jan 31, 2022) | ||
| 9-120866047-C-T | not specified | Uncertain significance (Apr 19, 2023) | ||
| 9-120866883-T-A | not specified | Uncertain significance (Feb 06, 2023) | ||
| 9-120866954-C-T | not specified | Uncertain significance (Sep 16, 2021) | ||
| 9-120869250-C-G | not specified | Uncertain significance (Jul 25, 2023) | ||
| 9-120869859-C-T | not specified | Uncertain significance (Sep 17, 2021) | ||
| 9-120869922-G-T | not specified | Uncertain significance (Dec 20, 2023) | ||
| 9-120870481-G-A | not specified | Uncertain significance (Feb 22, 2023) | ||
| 9-120870490-G-A | not specified | Uncertain significance (Nov 18, 2022) | ||
| 9-120870505-A-T | not specified | Uncertain significance (Apr 11, 2023) | ||
| 9-120870515-T-G | not specified | Uncertain significance (Jun 29, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PHF19 | protein_coding | protein_coding | ENST00000373896 | 14 | 21630 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000537 | 125743 | 0 | 5 | 125748 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.35 | 166 | 340 | 0.489 | 0.0000202 | 3754 |
| Missense in Polyphen | 30 | 118.42 | 0.25334 | 1229 | ||
| Synonymous | 0.981 | 123 | 138 | 0.894 | 0.00000810 | 1111 |
| Loss of Function | 5.00 | 3 | 34.9 | 0.0859 | 0.00000190 | 380 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Polycomb group (PcG) that specifically binds histone H3 trimethylated at 'Lys-36' (H3K36me3) and recruits the PRC2 complex. Probably involved in the transition from an active state to a repressed state in embryonic stem cells: acts by binding to H3K36me3, a mark for transcriptional activation, and recruiting H3K36me3 histone demethylases RIOX1 or KDM2B, leading to demethylation of H3K36 and recruitment of the PRC2 complex that mediates H3K27me3 methylation, followed by de novo silencing. Recruits the PRC2 complex to CpG islands and contributes to embryonic stem cell self-renewal. Also binds dimethylated at 'Lys- 36' (H3K36me2). Isoform 1 and isoform 2 inhibit transcription from an HSV-tk promoter. {ECO:0000269|PubMed:15563832, ECO:0000269|PubMed:21143197, ECO:0000269|PubMed:23104054, ECO:0000269|PubMed:23160351}.;
- Pathway
- Epigenetic regulation of gene expression;Gene expression (Transcription);PRC2 methylates histones and DNA
(Consensus)
Recessive Scores
- pRec
- 0.123
Intolerance Scores
- loftool
- 0.154
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.61
Haploinsufficiency Scores
- pHI
- 0.433
- hipred
- Y
- hipred_score
- 0.685
- ghis
- 0.527
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Phf19
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- chromatin organization;negative regulation of gene expression, epigenetic;positive regulation of transcription, DNA-templated;positive regulation of histone H3-K27 methylation
- Cellular component
- nucleoplasm;ESC/E(Z) complex
- Molecular function
- DNA-binding transcription factor activity;protein binding;nucleosome binding;methylated histone binding;sequence-specific DNA binding;metal ion binding