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

ClinVar

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

• Neurodevelopmental abnormality (18 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.

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				1		1
missense	2		44	3		49
nonsense	6					6
start loss						0
frameshift	9					9
inframe indel						0
splice donor/acceptor (+/-2bp)	1		1			2
splice region						0
non coding						0
Total	18	0	45	4	0

Highest pathogenic variant AF is 0.000112

Variants in PRMT9

This is a list of pathogenic ClinVar variants found in the PRMT9 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-147638545-G-A		not specified	Uncertain significance (Aug 05, 2024)
4-147638546-T-C		not specified	Uncertain significance (Apr 12, 2022)
4-147638605-A-G		not specified	Uncertain significance (Mar 14, 2023)
4-147638651-A-T		not specified	Uncertain significance (Dec 03, 2021)
4-147638665-G-A		Neurodevelopmental abnormality	Uncertain significance (Aug 02, 2022)
4-147638713-A-AT		Neurodevelopmental abnormality	Pathogenic (Aug 02, 2022)
4-147638727-TC-T		Neurodevelopmental abnormality	Pathogenic (Aug 02, 2022)
4-147639076-T-G		not specified	Uncertain significance (Sep 01, 2021)
4-147642797-T-C		not specified	Uncertain significance (May 31, 2023)
4-147642831-G-A		not specified	Uncertain significance (Sep 30, 2024)
4-147642846-C-T		not specified	Uncertain significance (Jul 25, 2024)
4-147642866-G-A		not specified	Uncertain significance (Dec 13, 2023)
4-147642879-C-G		not specified	Uncertain significance (Dec 13, 2022)
4-147653978-A-AC		Neurodevelopmental abnormality	Pathogenic (Aug 02, 2022)
4-147653981-T-C		not specified	Uncertain significance (Jul 15, 2024)
4-147654011-G-A		not specified	Uncertain significance (Apr 05, 2023)
4-147654016-G-C		not specified	Uncertain significance (Oct 29, 2024)
4-147654033-T-A		not specified	Uncertain significance (Sep 28, 2022)
4-147654050-C-T		not specified	Uncertain significance (Sep 20, 2023)
4-147654056-T-C		not specified	Uncertain significance (Apr 26, 2023)
4-147654057-G-C		not specified	Uncertain significance (Oct 08, 2024)
4-147654111-C-G		not specified	Likely benign (Dec 27, 2022)
4-147654111-C-T		not specified	Likely benign (Sep 01, 2021)
4-147654117-G-C		not specified	Uncertain significance (Nov 17, 2022)
4-147654125-A-G		Neurodevelopmental abnormality	Uncertain significance (Aug 02, 2022)

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