Is GRIN2B p.Pro680fs (c.2039del) pathogenic?

GRIN2B p.Pro680fs (c.2039del) is classified Pathogenic in GRIN2B (ClinVar, Single submitter, 1 submitter; last evaluated 2017-10-12). No gnomAD frequency available for this variant.

How common is GRIN2B p.Pro680fs (c.2039del) in the general population?

GRIN2B p.Pro680fs (c.2039del) is no gnomAD frequency available for this variant (gnomAD).

GRIN2B p.Pro680fs

c.2039del · rs1555103995 · VCV452935

Pathogenic Single submitter

Classification

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	predicted	premature termination codon in exon 11 of 14
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.4	GERP -0.5, 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.Pro680fs
Coding: c.2039del
MANE Select: NM_000834
dbSNP: rs1555103995
Type: Deletion
Location: chr12:13571936 (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.Pro680= Likely benign ★★ same residue
GRIN2B p.Gly543_Thr544del Likely pathogenic ★★ same type
GRIN2B p.Asn1224del Uncertain significance ★★ same type
GRIN2B c.2011-20_2011-17del Likely benign ★★ same type
GRIN2B c.2172-10del Benign/Likely benign ★★ same type
GRIN2B c.2010+1del Pathogenic ★ same type
GRIN2B c.2011-32_2014del Pathogenic ★ same type
GRIN2B p.Ala1318fs 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-pro680fs (accessed [today's date]).

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