PRMT1
protein arginine methyltransferase 1, the group of 7BS protein arginine methyltranferases|MicroRNA protein coding host genes
Basic information
Region (hg38): 19:49675786-49689029
Previous symbols: [ "HRMT1L2" ]
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 PRMT1 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 | 2 | |||||
| missense | 11 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 1 | 1 |
Variants in PRMT1
This is a list of pathogenic ClinVar variants found in the PRMT1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-49677009-C-G | Benign (Nov 02, 2020) | |||
| 19-49679878-G-C | not specified | Uncertain significance (May 02, 2024) | ||
| 19-49680524-A-G | not specified | Uncertain significance (Jul 31, 2023) | ||
| 19-49680526-G-C | not specified | Uncertain significance (Jul 08, 2022) | ||
| 19-49680531-G-A | Benign (Dec 31, 2019) | |||
| 19-49682052-G-A | not specified | Uncertain significance (Aug 20, 2024) | ||
| 19-49683938-A-G | not specified | Uncertain significance (Jun 04, 2024) | ||
| 19-49684755-C-T | not specified | Uncertain significance (Apr 25, 2022) | ||
| 19-49684815-G-A | not specified | Uncertain significance (Sep 16, 2021) | ||
| 19-49684978-G-C | not specified | Uncertain significance (May 14, 2024) | ||
| 19-49685023-G-A | not specified | Uncertain significance (Dec 08, 2022) | ||
| 19-49686174-G-A | not specified | Uncertain significance (Mar 20, 2023) | ||
| 19-49686649-A-C | not specified | Uncertain significance (Dec 22, 2023) | ||
| 19-49686674-C-T | not specified | Uncertain significance (Dec 28, 2023) | ||
| 19-49686675-G-A | Likely benign (Oct 01, 2022) | |||
| 19-49686685-A-G | not specified | Uncertain significance (Oct 13, 2021) | ||
| 19-49688235-G-A | not specified | Uncertain significance (Dec 15, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PRMT1 | protein_coding | protein_coding | ENST00000454376 | 11 | 13244 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000931 | 125648 | 0 | 1 | 125649 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.81 | 81 | 251 | 0.323 | 0.0000165 | 2474 |
| Missense in Polyphen | 14 | 73.766 | 0.18979 | 702 | ||
| Synonymous | -0.406 | 114 | 109 | 1.05 | 0.00000829 | 677 |
| Loss of Function | 4.17 | 0 | 20.2 | 0.00 | 9.56e-7 | 237 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Arginine methyltransferase that methylates (mono and asymmetric dimethylation) the guanidino nitrogens of arginyl residues present in proteins such as ESR1, histone H2, H3 and H4, PIAS1, HNRNPA1, HNRNPD, NFATC2IP, SUPT5H, TAF15, EWS, HABP4 and SERBP1 (PubMed:16879614, PubMed:26876602). Constitutes the main enzyme that mediates monomethylation and asymmetric dimethylation of histone H4 'Arg-4' (H4R3me1 and H4R3me2a, respectively), a specific tag for epigenetic transcriptional activation. Together with dimethylated PIAS1, represses STAT1 transcriptional activity, in the late phase of interferon gamma (IFN-gamma) signaling. May be involved in the regulation of TAF15 transcriptional activity, act as an activator of estrogen receptor (ER)-mediated transactivation, play a key role in neurite outgrowth and act as a negative regulator of megakaryocytic differentiation, by modulating p38 MAPK pathway. Methylates RBM15, promoting ubiquitination and degradation of RBM15 (PubMed:26575292). Methylates FOXO1 and retains it in the nucleus increasing its transcriptional activity. Methylates CHTOP and this methylation is critical for its 5-hydroxymethylcytosine (5hmC)-binding activity (PubMed:25284789). Methylates H4R3 in genes involved in glioblastomagenesis in a CHTOP- and/or TET1-dependent manner (PubMed:25284789). {ECO:0000269|PubMed:11387442, ECO:0000269|PubMed:11448779, ECO:0000269|PubMed:12718890, ECO:0000269|PubMed:16879614, ECO:0000269|PubMed:18320585, ECO:0000269|PubMed:18657504, ECO:0000269|PubMed:18773938, ECO:0000269|PubMed:19124016, ECO:0000269|PubMed:19136629, ECO:0000269|PubMed:19405910, ECO:0000269|PubMed:20442406, ECO:0000269|PubMed:25284789, ECO:0000269|PubMed:26575292, ECO:0000269|PubMed:26876602, ECO:0000269|PubMed:28040436}.;
- Pathway
- FoxO signaling pathway - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Energy Metabolism;mRNA Processing;Tryptophan metabolism;Interferon type I signaling pathways;Signal Transduction;Gene expression (Transcription);btg family proteins and cell cycle regulation;Generic Transcription Pathway;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;RMTs methylate histone arginines;Chromatin modifying enzymes;AndrogenReceptor;TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest;TP53 Regulates Transcription of Cell Cycle Genes;Signaling by Nuclear Receptors;Chromatin organization;Transcriptional Regulation by TP53;Direct p53 effectors;Estrogen-dependent gene expression;ESR-mediated signaling;Transcriptional regulation by RUNX1
(Consensus)
Recessive Scores
- pRec
- 0.459
Intolerance Scores
- loftool
- 0.0458
- rvis_EVS
- -0.56
- rvis_percentile_EVS
- 19.31
Haploinsufficiency Scores
- pHI
- 0.919
- hipred
- Y
- hipred_score
- 0.675
- ghis
- 0.697
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.971
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prmt1
- Phenotype
- reproductive system 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); embryo phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- prmt1
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- truncated
Gene ontology
- Biological process
- in utero embryonic development;regulation of transcription, DNA-templated;protein methylation;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;cell surface receptor signaling pathway;positive regulation of cell population proliferation;histone methylation;peptidyl-arginine methylation;peptidyl-arginine methylation, to asymmetrical-dimethyl arginine;neuron projection development;histone arginine methylation;histone H4-R3 methylation;positive regulation of erythrocyte differentiation;regulation of megakaryocyte differentiation;negative regulation of megakaryocyte differentiation;positive regulation of hemoglobin biosynthetic process;protein homooligomerization;positive regulation of p38MAPK cascade
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;methylosome
- Molecular function
- RNA binding;protein binding;methyltransferase activity;N-methyltransferase activity;protein methyltransferase activity;methyl-CpG binding;histone-arginine N-methyltransferase activity;protein-arginine N-methyltransferase activity;enzyme binding;protein-arginine omega-N monomethyltransferase activity;protein-arginine omega-N asymmetric methyltransferase activity;histone methyltransferase activity;identical protein binding;histone methyltransferase activity (H4-R3 specific);mitogen-activated protein kinase p38 binding;S-adenosyl-L-methionine binding