Is GRID2 p.Ter1008= (c.3023G>A) pathogenic?

GRID2 p.Ter1008= (c.3023G>A) is classified Likely benign in GRID2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-17). Ultra-rare (popmax 0.0343%, mid).

How common is GRID2 p.Ter1008= (c.3023G>A) in the general population?

GRID2 p.Ter1008= (c.3023G>A) is ultra-rare (popmax 0.0343%, mid) (gnomAD).

GRID2 p.Ter1008=

c.3023G>A · rs779594509 · VCV2414293

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

stop-loss

predicted LoF

gnomAD v4.1

Rare

ultra-rare (popmax 0.0343%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	stop-loss	predicted loss-of-function in a LoF-intolerant gene
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.9	GERP 1.7, phastCons 1
Overall
CADD	11.45	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0343% Middle Eastern · 2/5,828 alleles

Filtering AF 0.0216% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0208%

Overall 0.0191% 300/1,570,852 alleles · ultra-rare exomes 286/1,418,780 · genomes 14/152,072 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0343%	2,914
European (non-Finnish)	0.024%	4,169
Remaining individualsnot grpmax-eligible	0.0165%	6,050
Admixed American	0.00738%	13,544
Finnishnot grpmax-eligible	0.0048%	20,813
African / African-American	0.0041%	24,415

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: GRID2
Protein: p.Ter1008=
Coding: c.3023G>A
MANE Select: NM_001510
dbSNP: rs779594509
Type: single nucleotide variant
Location: chr4:93772497 (GRCh38)
Gene constraint: LOEUF 0.332 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.07 · 6 PDB

Full GRID2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GRID2 p.Ala654Thr Pathogenic/Likely pathogenic ★★ same type
GRID2 p.Thr649Ala Pathogenic/Likely pathogenic ★★ same type
GRID2 p.Ala196Glu Uncertain significance ★★ ⚠ same type
GRID2 p.Ala21Val Uncertain significance ★★ ⚠ same type
GRID2 p.Ala574Ser Uncertain significance ★★ ⚠ same type
GRID2 p.Arg229Gln Uncertain significance ★★ ⚠ same type
GRID2 p.Arg297Gln Uncertain significance ★★ ⚠ same type
GRID2 p.Arg300His 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/grid2-p-ter1008 (accessed [today's date]).

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