PRMT6

protein arginine methyltransferase 6, the group of 7BS protein arginine methyltranferases

Basic information

Region (hg38): 1:107056674-107067636

Previous symbols: [ "HRMT1L6" ]

Links

ENSG00000198890 ∙ NCBI:55170 ∙ OMIM:608274 ∙ HGNC:18241 ∙ Uniprot:Q96LA8 ∙ 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 PRMT6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRMT6 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			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	1	0

Variants in PRMT6

This is a list of pathogenic ClinVar variants found in the PRMT6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-107056708-C-T		PRMT6-related disorder	Likely benign (Feb 18, 2020)
1-107056729-A-G		not specified	Uncertain significance (Nov 26, 2024)
1-107056740-C-G		PRMT6-related disorder	Likely benign (Jan 03, 2023)
1-107056749-G-C		not specified	Uncertain significance (Oct 18, 2021)
1-107056749-G-T		not specified	Uncertain significance (Jan 30, 2024)
1-107056751-G-C		PRMT6-related disorder	Likely benign (Nov 14, 2019)
1-107056824-C-G		not specified	Uncertain significance (Feb 28, 2024)
1-107056842-C-T		not specified	Uncertain significance (Sep 27, 2024)
1-107056875-G-T		not specified	Uncertain significance (Mar 01, 2024)
1-107056951-C-T		not specified	Uncertain significance (Nov 15, 2024)
1-107057031-C-T		not specified	Uncertain significance (Nov 10, 2021)
1-107057037-G-A		not specified	Uncertain significance (Aug 19, 2024)
1-107057064-T-A		not specified	Uncertain significance (May 13, 2022)
1-107057110-G-A		not specified	Uncertain significance (Dec 08, 2023)
1-107057125-C-T		not specified	Uncertain significance (Oct 16, 2023)
1-107057165-T-A		not specified	Uncertain significance (Jul 08, 2022)
1-107057218-G-A		not specified	Uncertain significance (Dec 13, 2022)
1-107057251-A-G		not specified	Uncertain significance (Jun 11, 2024)
1-107057289-T-C		not specified	Uncertain significance (Jun 11, 2021)
1-107057296-C-T		PRMT6-related disorder	Benign (Oct 30, 2019)
1-107057312-G-C		not specified	Uncertain significance (Nov 08, 2022)
1-107057339-G-C		not specified	Uncertain significance (Nov 08, 2024)
1-107057346-G-C		not specified	Uncertain significance (Feb 27, 2024)
1-107057374-G-A		not specified	Uncertain significance (Jul 02, 2024)
1-107057403-C-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRMT6	protein_coding	protein_coding	ENST00000370078	1	2650

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00334	0.955	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.276	213	225	0.948	0.0000101	2374
Missense in Polyphen		58	72.134	0.80406		782
Synonymous	-2.04	128	102	1.26	0.00000470	815
Loss of Function	1.78	6	12.9	0.466	5.52e-7	131

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Arginine methyltransferase that can catalyze the formation of both omega-N monomethylarginine (MMA) and asymmetrical dimethylarginine (aDMA), with a strong preference for the formation of aDMA (PubMed:17898714, PubMed:18077460, PubMed:18079182, PubMed:19405910). Preferentially methylates arginyl residues present in a glycine and arginine-rich domain and displays preference for monomethylated substrates (PubMed:17898714, PubMed:18077460, PubMed:18079182, PubMed:19405910). Specifically mediates the asymmetric dimethylation of histone H3 'Arg-2' to form H3R2me2a (PubMed:17898714, PubMed:18079182, PubMed:18077460). H3R2me2a represents a specific tag for epigenetic transcriptional repression and is mutually exclusive with methylation on histone H3 'Lys-4' (H3K4me2 and H3K4me3) (PubMed:17898714, PubMed:18077460). Acts as a transcriptional repressor of various genes such as HOXA2, THBS1 and TP53 (PubMed:19509293). Repression of TP53 blocks cellular senescence (By similarity). Also methylates histone H2A and H4 'Arg-3' (H2AR3me and H4R3me, respectively). Acts as a regulator of DNA base excision during DNA repair by mediating the methylation of DNA polymerase beta (POLB), leading to the stimulation of its polymerase activity by enhancing DNA binding and processivity (PubMed:16600869). Methylates HMGA1 (PubMed:16157300, PubMed:16159886). Regulates alternative splicing events. Acts as a transcriptional coactivator of a number of steroid hormone receptors including ESR1, ESR2, PGR and NR3C1. Promotes fasting-induced transcriptional activation of the gluconeogenic program through methylation of the CRTC2 transcription coactivator. May play a role in innate immunity against HIV-1 in case of infection by methylating and impairing the function of various HIV-1 proteins such as Tat, Rev and Nucleocapsid protein p7 (NC) (PubMed:17267505). Methylates GPS2, protecting GPS2 from ubiquitination and degradation (By similarity). {ECO:0000250|UniProtKB:Q6NZB1, ECO:0000269|PubMed:11724789, ECO:0000269|PubMed:16157300, ECO:0000269|PubMed:16159886, ECO:0000269|PubMed:16600869, ECO:0000269|PubMed:17267505, ECO:0000269|PubMed:17898714, ECO:0000269|PubMed:18077460, ECO:0000269|PubMed:18079182, ECO:0000269|PubMed:19405910, ECO:0000269|PubMed:19509293, ECO:0000269|PubMed:20047962}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;RMTs methylate histone arginines;Chromatin modifying enzymes;Chromatin organization;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.202

Intolerance Scores

• loftool: 0.508
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.275
• hipred: Y
• hipred_score: 0.516
• ghis: 0.629

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: Prmt6
• Phenotype: cellular phenotype

Zebrafish Information Network

• Gene name: prmt6
• Affected structure: epiboly
• Phenotype tag: abnormal
• Phenotype quality: process quality

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;base-excision repair;regulation of transcription, DNA-templated;viral process;histone methylation;peptidyl-arginine methylation, to asymmetrical-dimethyl arginine;histone arginine methylation;histone H3-R2 methylation;histone H4-R3 methylation;regulation of megakaryocyte differentiation;negative regulation of transcription, DNA-templated;negative regulation of histone H3-K4 methylation;cellular senescence;regulation of signal transduction by p53 class mediator
• Cellular component: nucleus;nucleoplasm;nucleolus;cytosol
• Molecular function: chromatin binding;protein binding;histone-arginine N-methyltransferase activity;protein-arginine N-methyltransferase activity;protein-arginine omega-N monomethyltransferase activity;protein-arginine omega-N asymmetric methyltransferase activity;histone methyltransferase activity;histone binding;histone methyltransferase activity (H4-R3 specific);histone methyltransferase activity (H3-R2 specific);histone methyltransferase activity (H2A-R3 specific)