GeneBe

PRMT1

protein-coding

protein arginine methyltransferase 1, the group of 7BS protein arginine methyltranferases|MicroRNA protein coding host genes

Gene summary

This gene encodes a member of the protein arginine N-methyltransferase (PRMT) family. Post-translational modification of target proteins by PRMTs plays an important regulatory role in many biological processes, whereby PRMTs methylate arginine residues by transferring methyl groups from S-adenosyl-L-methionine to terminal guanidino nitrogen atoms. The encoded protein is a type I PRMT and is responsible for the majority of cellular arginine methylation activity. Increased expression of this gene may play a role in many types of cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 5. [provided by RefSeq, Dec 2011]

Previous symbols:
  • HRMT1L2

MANE transcript

NM_001536.6

Inheritance

—

ClinVar variants

U:32B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr19:49,675,786-49,689,029

External References & Databases

Ensembl (ENSG00000126457)NCBI Gene (3276)OMIM (602950)HGNC:5187GenCCUniProt (Q99873)AlphaFoldClinVar (PRMT1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~13.2 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRMT1 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 22
not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001536.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
1
clinvar
 3
missense
25
clinvar
 25
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
6
clinvar
 6
Total00321134
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 92 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001536.6RefSeqNP_001527.311MANE Select
ENST00000454376.7EnsemblENSP00000406162.211MANE Select
NM_001207042.3RefSeqNP_001193971.18Standard
NM_198318.5RefSeqNP_938074.210Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
prmt1Danio rerio

Structure: post-vent region

Quality: truncated

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • FoxO signaling pathway - Homo sapiens (human)
  • Glucagon signaling pathway - Homo sapiens (human)
  • Energy Metabolism
  • mRNA Processing
  • Tryptophan metabolism

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

Molecular Function

  • RNA binding
  • protein binding
  • methyltransferase activity
  • N-methyltransferase activity
  • protein methyltransferase activity

Cellular Component

  • nucleus
  • nucleoplasm
  • cytoplasm
  • cytosol
  • methylosome

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000454376
Coding exons
11
Length
13244
Individuals with no LoFs
125648
Homozygous LoFs
0
Heterozygous LoFs
1
Defined
125649
p
0.00000398
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.81812510.3230.00001652474
Missense (PolyPhen)1473.7660.18979702
Synonymous-0.4061141091.050.00000829677
Loss of Function4.17020.20.009.56e-7237

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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}.;

Recessive Scores

pRec
0.459

Intolerance Scores

LoFtool
0.0458
RVIS EVS
-0.56
RVIS percentile EVS
19.31

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.971

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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