Is IGF2 p.Glu30fs (c.89_98del) pathogenic?

IGF2 p.Glu30fs (c.8998del) is classified Pathogenic in IGF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-05). No gnomAD frequency available for this variant.

How common is IGF2 p.Glu30fs (c.89_98del) in the general population?

IGF2 p.Glu30fs (c.89_98del) is no gnomAD frequency available for this variant (gnomAD).

IGF2 p.Glu30fs

c.89_98del · rs2495590166 · VCV2134425

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 LoF-intolerant gene
NMD	predicted	premature termination codon in exon 2 of 4
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.92	GERP -3.3

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: IGF2
Protein: p.Glu30fs
Coding: c.89_98del
MANE Select: NM_000612
dbSNP: rs2495590166
Type: Deletion
Location: chr11:2135426 (GRCh38)
Gene constraint: LOEUF 0.496 · pLI 0.96 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 58.95 · 16 PDB
Residue 30: a UniProt-annotated variant site (in srs3); the 'b' region

Full IGF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

IGF2 p.Thr30= Benign ★ same residue
IGF2 p.Pro157_Leu158insTer Uncertain significance ★★ same type
IGF2 p.Arg61_Arg62insTer Likely pathogenic ★ same type
IGF2 p.Asp76fs Likely pathogenic ★ same type
IGF2 p.Glu36fs Likely pathogenic ★ same type
IGF2 p.Ile66fs Likely pathogenic ★ same type
IGF2 c.158-20_158-17del Uncertain significance ★ same type
IGF2 p.Cys75fs 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/igf2-p-glu30fs (accessed [today's date]).

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