Is PRMT9 p.Ile245fs (c.734_735del) pathogenic?

PRMT9 p.Ile245fs (c.734735del) is classified Pathogenic in PRMT9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-02). Associated with PRMT9-associated neurodevelopmental disorder.

What condition is associated with PRMT9 p.Ile245fs (c.734_735del)?

PRMT9 p.Ile245fs (c.734_735del) is associated with PRMT9-associated neurodevelopmental disorder (ClinVar).

PRMT9 p.Ile245fs

c.734_735del · VCV4530584

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

PRMT9-associated neurodevelopmental disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: PRMT9
Protein: p.Ile245fs
Coding: c.734_735del
MANE Select: NM_138364
Type: Deletion
Location: chr4:147672967 (GRCh38)
Gene constraint: LOEUF 0.91 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.94 · 4 PDB
Residue 245: a β-strand; the sam-dependent mtase prmt-type 1 domain

Full PRMT9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

PRMT9-associated neurodevelopmental disorder

Similar variants

PRMT9 p.Glu264Asp Uncertain significance ★ ⚠ same condition
PRMT9 p.Ile170Thr Uncertain significance ★ ⚠ same condition
PRMT9 p.Trp152Ter Uncertain significance ★ same condition
PRMT9 c.(846+1_847-1 Pathogenic ★ same type
PRMT9 p.Gln382fs Pathogenic ★ same type
PRMT9 p.Gly781fs Pathogenic ★ same type
PRMT9 p.Leu182fs Pathogenic ★ same type
PRMT9 p.Leu279fs Pathogenic ★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/prmt9-p-ile245fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown