PRMT9

protein arginine methyltransferase 9, the group of 7BS protein arginine methyltranferases

Basic information

Region (hg38): 4:147637785-147684163

Previous symbols: [ "PRMT10" ]

Links

ENSG00000164169 ∙ NCBI:90826 ∙ OMIM:616125 ∙ HGNC:25099 ∙ Uniprot:Q6P2P2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (Limited), mode of inheritance: AR
• neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRMT9 gene.

• not_specified (98 variants)
• Neurodevelopmental_abnormality (22 variants)
• not_provided (5 variants)
• Meckel_syndrome,_type_9 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRMT9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000138364.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense	1	2	97	4		104
nonsense	6					6
start loss						0
frameshift	9					9
splice donor/acceptor (+/-2bp)	1		1			2
Total	17	2	98	5	0

Highest pathogenic variant AF is 0.000044628025

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRMT9	protein_coding	protein_coding	ENST00000322396	12	46446

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.53e-12	0.866	125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	376	453	0.831	0.0000218	5591
Missense in Polyphen		102	158.08	0.64523		1970
Synonymous	1.54	137	162	0.846	0.00000804	1591
Loss of Function	1.90	24	36.4	0.660	0.00000161	480

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000627	0.000626
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000435	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000327	0.000316
Middle Eastern	0.000435	0.000435
South Asian	0.000294	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Arginine methyltransferase that can both catalyze the formation of omega-N monomethylarginine (MMA) and symmetrical dimethylarginine (sDMA). Specifically mediates the symmetrical dimethylation of SF3B2. Involved in the regulation of alternative splicing of pre-mRNA (PubMed:25737013, PubMed:25979344). {ECO:0000269|PubMed:25737013, ECO:0000269|PubMed:25979344}.

Intolerance Scores

• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.45

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.324
• ghis: 0.527

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Prmt9

Gene ontology

• Biological process: regulation of transcription, DNA-templated;mRNA processing;peptidyl-arginine methylation, to symmetrical-dimethyl arginine;peptidyl-arginine methylation, to asymmetrical-dimethyl arginine;histone arginine methylation
• Cellular component: cytoplasm;cytosol
• Molecular function: 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;protein-arginine omega-N symmetric methyltransferase activity