PRMT2

protein-coding

protein arginine methyltransferase 2, the group of 7BS protein arginine methyltranferases

Gene summary

Enables several functions, including nuclear receptor binding activity; peroxisome proliferator activated receptor binding activity; and protein homodimerization activity. Involved in negative regulation of inflammatory response; positive regulation of DNA-templated transcription; and regulation of intracellular signal transduction. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

HRMT1L1

MANE transcript

NM_206962.4

Inheritance

—

ClinVar variants

U:57B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr21:46,635,595-46,665,685

External References & Databases

Ensembl (ENSG00000160310)

Transcript & Mutation Effects

hg38 • Region Span ~30.1 kb

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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 PRMT2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 52

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_206962.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar	1 clinvar	4
missense			51 clinvar	4 clinvar	1 clinvar	56
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	57	6	2	65

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 217 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_206962.4	RefSeq	NP_996845.1	10	MANE Select
ENST00000355680.8	Ensembl	ENSP00000347906.3	10	MANE Select
NM_001242864.3	RefSeq	NP_001229793.1	8	Standard
NM_001242865.3	RefSeq	NP_001229794.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Retinoblastoma (RB) in Cancer
mRNA Processing
AndrogenReceptor

Biological Process

regulation of transcription, DNA-templated
protein methylation
signal transduction
histone methylation
peptidyl-arginine methylation, to asymmetrical-dimethyl arginine

Molecular Function

transcription coactivator activity
protein binding
histone-arginine N-methyltransferase activity
protein-arginine N-methyltransferase activity
estrogen receptor binding

Cellular Component

nucleus
nucleoplasm
nucleolus
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397637
Coding exons: 10
Length: 29958
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125748
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.79	174	254	0.684	0.0000151	2834
Missense (PolyPhen)		70	113.48	0.61683		1282
Synonymous	-0.0223	111	111	1.00	0.00000823	803
Loss of Function	2.84	9	24.1	0.374	0.00000117	266

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.000096	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00013	0.00013	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Arginine methyltransferase that methylates the guanidino nitrogens of arginyl residues in proteins such as STAT3, FBL, histone H4. Acts as a coactivator (with NCOA2) of the androgen receptor (AR)-mediated transactivation. Acts as a coactivator (with estrogen) of estrogen receptor (ER)-mediated transactivation. Enhances PGR, PPARG, RARA-mediated transactivation. May inhibit NF-kappa-B transcription and promote apoptosis. Represses E2F1 transcriptional activity (in a RB1- dependent manner). May be involved in growth regulation. {ECO:0000269|PubMed:12039952, ECO:0000269|PubMed:16648481, ECO:0000269|PubMed:17587566, ECO:0000269|PubMed:19405910}.;

Recessive Scores

pRec: 0.235

Intolerance Scores

LoFtool: 0.750
RVIS EVS: -0.02
RVIS percentile EVS: 52.09

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.987

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium