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Relevance to Autism

Kroll-Hermi et al., 2025 reported 35 individuals from 26 families with biallelic loss-of-function variants in PRMT9 presenting with a neurodevelopmental disorder characterized by global developmental delay, learning disabilities, mild to severe intellectual disability, autism spectrum disorder, epilepsy, and hypotonia; skin fibroblasts from affected individuals exhibited reduced expression at the RNA and/or protein level and subsequent aberrant methylation activity, as well as anomalies in the length of primary cilia under ciliogenesis conditions, while a prmt9 knockout zebrafish model displayed abnormal social preference in adult animals. A de novo loss-of-function variant and a de novo missense variant in PRMT9 had previously been reported in ASD probands from the SPARK cohort (Zhou et al., 2022). Using a Prmt9 conditional knockout (cKO) mouse, Shen et al., 2024 demonstrated that knockout of Prmt9 in hippocampal neurons caused alternative splicing of ~1900 genes, which likely accounted for the aberrant synapse development and impaired learning and memory observed in Prmt9 cKO mice; furthermore, the authors identified a methylation-sensitive protein-RNA interaction between the arginine 508 (R508) of the splicing factor SF3B2, the site that is exclusively methylated by PRMT9, and the pre-mRNA anchoring site, a cis-regulatory element that is critical for RNA splicing.

Molecular Function

This gene encodes a type II methyltransferase. Post-translational modification of target proteins by PRMTs plays an important regulatory role in many biological processes, whereby PRMTs methylate arginine residues by transferring methyl groups from S-adenosyl-L-methionine to the guanidino nitrogen atoms of arginine. The protein encoded by this gene methylates spliceosome associated protein 145 to regulate alternative splicing and acts as a modulator of small nuclear ribonucleoprotein maturation.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Bi-allelic PRMT9 loss-of-function variants cause a syndromic form of intellectual disability
DD, ID
ASD, epilepsy/seizures
Support
Loss-of-function mutation in PRMT9 causes abnormal synapse development by dysregulation of RNA alternative splicing
ID
Support
Integrating de novo and inherited variants in 42
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1531R001a 
 frameshift_variant 
 c.545delT 
 p.Leu182TrpfsTer10 
 Familial 
 Both parents 
 Simplex 
 GEN1531R002a 
 missense_variant 
 c.565G>A 
 p.Gly189Arg 
 Familial 
 Both parents 
 Multiplex 
 GEN1531R003a 
 missense_variant 
 c.554G>A 
 p.Gly185Glu 
 Familial 
 Paternal 
 Multiplex 
 GEN1531R003b 
 stop_gained 
 c.1318C>T 
 p.Gln440Ter 
 Familial 
 Maternal 
 Multiplex 
 GEN1531R004a 
 frameshift_variant 
 c.491delC 
 p.Thr164LysfsTer28 
 Familial 
 Both parents 
 Simplex 
 GEN1531R005a 
 frameshift_variant 
 c.1918dup 
 p.Val640GlyfsTer4 
 Familial 
 Both parents 
 Multiplex 
 GEN1531R006a 
 stop_gained 
 c.1075C>T 
 p.Arg359Ter 
 Familial 
 Both parents 
 Simplex 
 GEN1531R007a 
 copy_number_loss 
 c.(846+1_847-1)_(1330+1_1331-1)del 
 p.Lys284ThrfsTer3 
 Familial 
 Both parents 
 Simplex 
 GEN1531R008a 
 frameshift_variant 
 c.258_261delACTT 
 p.Leu87ValfsTer15 
 Unknown 
  
 Unknown 
 GEN1531R009a 
 stop_gained 
 c.415G>T 
 p.Glu139Ter 
 Familial 
 Maternal 
 Simplex 
 GEN1531R009b 
 missense_variant 
 c.554G>A 
 p.Gly185Glu 
 Familial 
 Paternal 
 Simplex 
 GEN1531R010a 
 stop_gained 
 c.257T>A 
 p.Leu86Ter 
 Familial 
 Paternal 
 Multiplex 
 GEN1531R010b 
 frameshift_variant 
 c.1143delT 
 p.Gln382ArgfsTer3 
 Familial 
 Maternal 
 Multiplex 
 GEN1531R011a 
 missense_variant 
 c.1144C>A 
 p.Gln382Lys 
 Familial 
 Both parents 
 Simplex 
 GEN1531R012a 
 frameshift_variant 
 c.491delC 
 p.Thr164LysfsTer28 
 Familial 
 Both parents 
 Simplex 
 GEN1531R013a 
 splice_site_variant 
 c.576-2A>G 
 p.? 
 Familial 
 Both parents 
 Simplex 
 GEN1531R014a 
 stop_gained 
 c.219G>A 
 p.Trp73Ter 
 Familial 
 Maternal 
 Simplex 
 GEN1531R014b 
 frameshift_variant 
 c.836delT 
 p.Leu279TyrfsTer30 
 Familial 
 Paternal 
 Simplex 
 GEN1531R015a 
 missense_variant 
 c.1772T>C 
 p.Phe591Ser 
 Familial 
 Both parents 
 Multiplex 
 GEN1531R016a 
 missense_variant 
 c.773A>T 
 p.Asp258Val 
 Familial 
 Both parents 
 Simplex 
 GEN1531R017a 
 frameshift_variant 
 c.106_107del 
 p.Leu36GlyfsTer39 
 Familial 
 Maternal 
 Simplex 
 GEN1531R017b 
 stop_gained 
 c.270T>G 
 p.Tyr90Ter 
 Familial 
 Paternal 
 Simplex 
 GEN1531R018a 
 frameshift_variant 
 c.2356dup 
 p.Ile786AsnfsTer10 
 Familial 
 Both parents 
 Simplex 
 GEN1531R019a 
 missense_variant 
 c.773A>T 
 p.Asp258Val 
 Familial 
 Maternal 
 Simplex 
 GEN1531R019b 
 frameshift_variant 
 c.2342delG 
 p.Gly781GlufsTer3 
 Unknown 
  
 Simplex 
 GEN1531R020a 
 stop_gained 
 c.257T>A 
 p.Leu86Ter 
 Familial 
 Both parents 
 Simplex 
 GEN1531R021a 
 missense_variant 
 c.2405C>T 
 p.Thr802Ile 
 Familial 
 Both parents 
 Simplex 
 GEN1531R022a 
 frameshift_variant 
 c.491delC 
 p.Thr164LysfsTer28 
 Familial 
 Both parents 
 Simplex 
 GEN1531R023a 
 frameshift_variant 
 c.2116_2117del 
 p.Gln706AspfsTer24 
 Familial 
 Both parents 
 Simplex 
 GEN1531R024a 
 copy_number_loss 
 c.(846+1_847-1)_(1330+1_1331-1)del 
 p.Lys284ThrfsTer3 
 Familial 
 Both parents 
 Multiplex 
 GEN1531R025a 
 splice_site_variant 
 c.847-10_849del 
 p.? 
 Familial 
 Both parents 
 Multiplex 
 GEN1531R026 
 copy_number_gain 
 c.(1330+1_1331-1)_(*747_?)dup 
 p.? 
 Unknown 
  
 Simplex 
 GEN1531R027 
 splice_site_variant 
 c.2322+1G>A 
 p.? 
 De novo 
  
 Unknown 
 GEN1531R028 
 missense_variant 
 c.907A>T 
 p.Ile303Leu 
 De novo 
  
 Unknown 
 GEN1531R029 
 stop_gained 
 c.1075C>T 
 p.Arg359Ter 
 Familial 
 Maternal 
 Multiplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
4
Duplication
 1
 
4
Duplication
 1
 
4
Duplication
 1
 
4
Duplication
 1
 
4
Duplication
 1
 
4
Deletion
 1
 
4
Deletion-Duplication
 9
 
4
Duplication
 1
 

No Animal Model Data Available

No PIN Data Available
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