How common is GRIN1 p.Arg489= (c.1467G>T) in the general population?

GRIN1 p.Arg489= (c.1467G>T) is no allele count reported in gnomAD v4.1 (AN 1,611,560) (gnomAD).

GRIN1 p.Arg489=

Q: Is GRIN1 p.Arg489= (c.1467G>T) pathogenic?

GRIN1 p.Arg489= (c.1467G>T) is classified Likely benign in GRIN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-01). No allele count reported in gnomAD v4.1 (AN 1,611,560); Associated with neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant.

Q: What condition is associated with GRIN1 p.Arg489= (c.1467G>T)?

GRIN1 p.Arg489= (c.1467G>T) is associated with neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant (ClinVar).

c.1467G>T · rs772351282 · VCV1563784

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,611,560)

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/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.37	donor gain · deltas
Pangolin	Δ0.59	loss · gain 0.29 · SpliceAI calls gain · independent
Constraint at this position
Conservation	phyloP 11	GERP -3.4, phastCons 1
Overall
CADD	24.4	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,611,560). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: GRIN1
Protein: p.Arg489=
Coding: c.1467G>T
MANE Select: NM_007327
dbSNP: rs772351282
Type: single nucleotide variant
Location: chr9:137161416 (GRCh38)
Structure: AlphaFold pLDDT 44.02
Residue 489: 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-arg489 (accessed [today's date]).

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