Is GRIN1 p.Phe784= (c.2352C>T) pathogenic?

GRIN1 p.Phe784= (c.2352C>T) is classified Likely benign in GRIN1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-03-01). Very rare (popmax 0.00322%, nfe); Associated with neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant.

How common is GRIN1 p.Phe784= (c.2352C>T) in the general population?

GRIN1 p.Phe784= (c.2352C>T) is very rare (popmax 0.00322%, nfe) (gnomAD).

GRIN1 p.Phe784=

Q: What condition is associated with GRIN1 p.Phe784= (c.2352C>T)?

GRIN1 p.Phe784= (c.2352C>T) is associated with neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant (ClinVar).

c.2352C>T · rs763771717 · VCV1126407

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00322%, nfe)

Conditions

neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.1	GERP 0.4, phastCons 1
Overall
CADD	14.58	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00322% European (non-Finnish) · 38/1,179,074 alleles

Filtering AF 0.0024% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0021%

Overall 0.00242% 39/1,612,568 alleles · very rare exomes 35/1,460,376 · genomes 4/152,192 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00322%	31,028
Remaining individualsnot grpmax-eligible	0.0016%	62,448

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: GRIN1
Protein: p.Phe784=
Coding: c.2352C>T
MANE Select: NM_007327
dbSNP: rs763771717
Type: single nucleotide variant
Location: chr9:137163577 (GRCh38)
Structure: AlphaFold pLDDT 44.02
Residue 784: the 'disordered' region

Full GRIN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GRIN1 p.Arg659Gln Pathogenic/Likely pathogenic ★★ same condition
GRIN1 p.Arg659Trp Pathogenic ★★ same condition
GRIN1 p.Arg794Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
GRIN1 p.Arg844Cys Pathogenic/Likely pathogenic ★★ same condition
GRIN1 p.Arg844Leu Pathogenic/Likely pathogenic ★★ same condition
GRIN1 p.Asp227His Likely pathogenic ★★ same condition
GRIN1 p.Asp732Glu Pathogenic/Likely pathogenic ★★ same condition
GRIN1 p.Gly618Arg Likely pathogenic ★★ same condition

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/grin1-p-phe784 (accessed [today's date]).

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