Is GRIN2B p.Arg900fs (c.2674_2698dup) pathogenic?

GRIN2B p.Arg900fs (c.26742698dup) is classified Likely pathogenic in GRIN2B (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-01). No gnomAD frequency available for this variant.

How common is GRIN2B p.Arg900fs (c.2674_2698dup) in the general population?

GRIN2B p.Arg900fs (c.2674_2698dup) is no gnomAD frequency available for this variant (gnomAD).

GRIN2B p.Arg900fs

c.2674_2698dup · rs2136406273 · VCV1298535

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon in the last exon (14 of 14) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 0.69, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: GRIN2B
Protein: p.Arg900fs
Coding: c.2674_2698dup
MANE Select: NM_000834
dbSNP: rs2136406273
Type: Duplication
Location: chr12:13564539 (GRCh38)
Gene constraint: LOEUF 0.102 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 60.66 · 36 PDB

Full GRIN2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GRIN2B p.Arg900Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
GRIN2B p.Arg900His Uncertain significance ★ ⚠ same residue
GRIN2B p.Arg900= Benign ★ same residue
GRIN2B c.1125+6_1125+10dup Likely benign ★★ same type
GRIN2B c.1655-12dup Benign/Likely benign ★★ same type
GRIN2B c.2011-2_2038dup Likely pathogenic ★ same type
GRIN2B c.2352_2359+2dup Pathogenic ★ same type
GRIN2B p.Glu500_Val501insProGlyMetValTer Pathogenic ★ 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/grin2b-p-arg900fs (accessed [today's date]).

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