Is GRIK2 p.Arg900= (c.2700G>A) pathogenic?

GRIK2 p.Arg900= (c.2700G>A) is classified Likely benign in GRIK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-11-30). Very rare (popmax 0.0011%, sas).

How common is GRIK2 p.Arg900= (c.2700G>A) in the general population?

GRIK2 p.Arg900= (c.2700G>A) is very rare (popmax 0.0011%, sas) (gnomAD).

GRIK2 p.Arg900=

c.2700G>A · VCV4893624

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

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 8.6	GERP 2.5, phastCons 1
Overall
CADD	11.81	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/90,986 alleles

Filtering AF 0.000247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000159%

Overall 0.000496% 8/1,611,618 alleles · very rare exomes 8/1,459,608 · genomes 0/152,010 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0011%	90,986
European (non-Finnish)	0.000594%	168,354

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: GRIK2
Protein: p.Arg900=
Coding: c.2700G>A
MANE Select: NM_021956
Type: single nucleotide variant
Location: chr6:102068484 (GRCh38)
Gene constraint: LOEUF 0.477 · pLI 0.99 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.67 · 2 PDB

Full GRIK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GRIK2 p.Arg900Met Uncertain significance ★ ⚠ same residue
GRIK2 p.Arg900Ser Uncertain significance ★ ⚠ same residue
GRIK2 p.Ala657Thr Pathogenic ★★ same type
GRIK2 p.Arg184His Uncertain significance ★★ ⚠ same type
GRIK2 p.Arg543His Uncertain significance ★★ ⚠ same type
GRIK2 p.Arg775Gln Uncertain significance ★★ ⚠ same type
GRIK2 p.Asn123Ser Uncertain significance ★★ ⚠ same type
GRIK2 p.Asp493Gly Uncertain significance ★★ ⚠ 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/grik2-p-arg900 (accessed [today's date]).

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