PRMT2

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

Basic information

Region (hg38): 21:46635595-46665685

Previous symbols: [ "HRMT1L1" ]

Links

ENSG00000160310 ∙ NCBI:3275 ∙ OMIM:601961 ∙ HGNC:5186 ∙ Uniprot:P55345 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRMT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRMT2 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	1	3
missense			13	3	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	13	5	2

Variants in PRMT2

This is a list of pathogenic ClinVar variants found in the PRMT2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
21-46643538-G-A		not specified	Uncertain significance (Nov 03, 2022)
21-46643548-C-T		not specified	Likely benign (Nov 21, 2024)
21-46643557-G-T		not specified	Uncertain significance (Sep 22, 2023)
21-46643596-A-T		not specified	Uncertain significance (Jun 30, 2023)
21-46643598-T-C		not specified	Uncertain significance (Oct 12, 2024)
21-46643619-G-A		not specified	Uncertain significance (Sep 20, 2023)
21-46644328-A-C		not specified	Uncertain significance (Feb 22, 2023)
21-46644375-C-T		not specified	Uncertain significance (Aug 20, 2024)
21-46644376-G-A		not specified	Uncertain significance (Mar 20, 2024)
21-46644400-C-T		not specified	Uncertain significance (Jun 02, 2024)
21-46644470-C-T			Likely benign (Feb 01, 2023)
21-46644477-T-A		not specified	Uncertain significance (Jul 31, 2024)
21-46644495-C-T			Benign (May 21, 2018)
21-46648497-A-G		not specified	Uncertain significance (Nov 15, 2021)
21-46648534-C-T		not specified	Uncertain significance (Dec 28, 2022)
21-46649582-C-T		not specified	Uncertain significance (Jul 26, 2024)
21-46649679-T-C			Likely benign (Aug 02, 2018)
21-46649691-C-T			Benign (Jul 02, 2018)
21-46649698-G-A		not specified	Uncertain significance (Dec 17, 2021)
21-46649728-A-C		not specified	Uncertain significance (May 14, 2024)
21-46658821-T-C		not specified	Likely benign (Oct 26, 2022)
21-46658854-A-T		not specified	Uncertain significance (Dec 06, 2024)
21-46658866-G-A		not specified	Likely benign (May 31, 2022)
21-46658880-T-C		not specified	Uncertain significance (Mar 30, 2024)
21-46658913-G-A		not specified	Uncertain significance (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRMT2	protein_coding	protein_coding	ENST00000397637	10	29958

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00161	0.997	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	174	254	0.684	0.0000151	2834
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000159	0.000158
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000471	0.0000462
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.000132	0.000131
Other	0.000174	0.000163

dbNSFP

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}.
• Pathway: Retinoblastoma (RB) in Cancer;mRNA Processing;AndrogenReceptor (Consensus)

Recessive Scores

• pRec: 0.235

Intolerance Scores

• loftool: 0.750
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.09

Haploinsufficiency Scores

• pHI: 0.173
• hipred: Y
• hipred_score: 0.775
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prmt2
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; skeleton 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)

Gene ontology

• Biological process: regulation of transcription, DNA-templated;protein methylation;signal transduction;histone methylation;peptidyl-arginine methylation, to asymmetrical-dimethyl arginine;negative regulation of NF-kappaB transcription factor activity;histone arginine methylation;positive regulation of apoptotic process;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;developmental cell growth;regulation of androgen receptor signaling pathway;negative regulation of G1/S transition of mitotic cell cycle
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol
• Molecular function: transcription coactivator activity;protein binding;histone-arginine N-methyltransferase activity;protein-arginine N-methyltransferase activity;estrogen receptor binding;progesterone receptor binding;protein-arginine omega-N asymmetric methyltransferase activity;histone methyltransferase activity;protein homodimerization activity;retinoic acid receptor binding;peroxisome proliferator activated receptor binding;protein-containing complex binding;thyroid hormone receptor binding;androgen receptor binding