Is GRIN1 p.Arg52= (c.156G>T) pathogenic?

GRIN1 p.Arg52= (c.156G>T) is classified Likely benign in GRIN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-16). Very rare (popmax 0.00167%, amr); Associated with neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant.

How common is GRIN1 p.Arg52= (c.156G>T) in the general population?

GRIN1 p.Arg52= (c.156G>T) is very rare (popmax 0.00167%, amr) (gnomAD).

GRIN1 p.Arg52=

Q: What condition is associated with GRIN1 p.Arg52= (c.156G>T)?

GRIN1 p.Arg52= (c.156G>T) is associated with neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant (ClinVar).

c.156G>T · rs202166785 · VCV1568945

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

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 -0.044	GERP -2.5, phastCons 0.25
Overall
CADD	7.184	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,024 alleles

Overall 6.2e-05% 1/1,613,862 alleles · very rare exomes 1/1,461,564 · genomes 0/152,298 · joint denominator

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.Arg52=
Coding: c.156G>T
MANE Select: NM_007327
dbSNP: rs202166785
Type: single nucleotide variant
Location: chr9:137139642 (GRCh38)
Structure: AlphaFold pLDDT 44.02
Residue 52: 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.Arg52Gln Uncertain significance ★ ⚠ same residue
GRIN1 p.Arg52Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
GRIN1 p.Arg52Pro Likely benign ★ same residue
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

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-arg52 (accessed [today's date]).

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