PRMT8

protein arginine methyltransferase 8, the group of 7BS protein arginine methyltranferases

Basic information

Region (hg38): 12:3381348-3593973

Previous symbols: [ "HRMT1L3", "HRMT1L4" ]

Links

ENSG00000111218 ∙ NCBI:56341 ∙ OMIM:610086 ∙ HGNC:5188 ∙ Uniprot:Q9NR22 ∙ 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 PRMT8 gene.

• Inborn genetic diseases (10 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRMT8 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					3	3
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	3

Variants in PRMT8

This is a list of pathogenic ClinVar variants found in the PRMT8 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-3491674-G-A		not specified	Uncertain significance (Oct 29, 2021)
12-3540628-C-G		not specified	Uncertain significance (Apr 05, 2023)
12-3540631-C-T		not specified	Uncertain significance (Feb 15, 2023)
12-3540632-C-G			Benign (Mar 29, 2018)
12-3540764-C-T			Benign (Mar 29, 2018)
12-3568750-G-A		not specified	Uncertain significance (May 18, 2022)
12-3569519-G-A		not specified	Uncertain significance (Nov 07, 2022)
12-3576915-G-A		not specified	Uncertain significance (Jan 11, 2023)
12-3583083-C-T		not specified	Uncertain significance (Jun 01, 2023)
12-3583127-C-T		not specified	Uncertain significance (Dec 05, 2022)
12-3583145-G-A		not specified	Uncertain significance (Nov 10, 2022)
12-3592297-G-A		not specified	Uncertain significance (Aug 12, 2021)
12-3592301-G-A			Benign (Jul 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRMT8	protein_coding	protein_coding	ENST00000382622	10	212625

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.980	0.0198	124782	1	961	125744	0.00383

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.46	87	237	0.368	0.0000133	2619
Missense in Polyphen		8	73.01	0.10957		775
Synonymous	0.280	91	94.5	0.963	0.00000609	708
Loss of Function	3.82	2	20.8	0.0961	9.65e-7	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0127	0.0126
Ashkenazi Jewish	0.00770	0.00617
East Asian	0.00313	0.00289
Finnish	0.00418	0.00407
European (Non-Finnish)	0.00225	0.00209
Middle Eastern	0.00313	0.00289
South Asian	0.00559	0.00504
Other	0.00703	0.00621

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionine-dependent and membrane- associated arginine methyltransferase that can both catalyze the formation of omega-N monomethylarginine (MMA) and asymmetrical dimethylarginine (aDMA) in proteins such as NIFK, myelin basic protein, histone H4, H2A and H2A/H2B dimer (PubMed:16051612, PubMed:17925405, PubMed:26876602, PubMed:26529540). Able to mono- and dimethylate EWS protein; however its precise role toward EWS remains unclear as it still interacts with fully methylated EWS (PubMed:18320585). {ECO:0000269|PubMed:16051612, ECO:0000269|PubMed:17925405, ECO:0000269|PubMed:18320585, ECO:0000269|PubMed:26529540, ECO:0000269|PubMed:26876602}.

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.278
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.259
• hipred: Y
• hipred_score: 0.731
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prmt8
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: prmt8b
• Affected structure: Purkinje cell
• Phenotype tag: abnormal
• Phenotype quality: decreased branchiness

Gene ontology

• Biological process: regulation of transcription, DNA-templated;protein methylation;histone methylation;peptidyl-arginine methylation;peptidyl-arginine methylation, to asymmetrical-dimethyl arginine;histone arginine methylation;regulation of protein binding;protein homooligomerization
• Cellular component: nucleus;cytosol;plasma membrane;anchored component of the cytoplasmic side of the plasma membrane
• Molecular function: protein binding;histone-arginine N-methyltransferase activity;S-adenosylmethionine-dependent methyltransferase activity;protein-arginine omega-N monomethyltransferase activity;protein-arginine omega-N asymmetric methyltransferase activity;identical protein binding;protein homodimerization activity;protein heterodimerization activity;S-adenosyl-L-methionine binding