Is IGF2 p.Cys33Arg (c.97T>C) pathogenic?

IGF2 p.Cys33Arg (c.97T>C) is classified Likely pathogenic in IGF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-06-23). AlphaMissense: likely pathogenic (0.9913); Absent from gnomAD v4.1.

How common is IGF2 p.Cys33Arg (c.97T>C) in the general population?

IGF2 p.Cys33Arg (c.97T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about IGF2 p.Cys33Arg (c.97T>C)?

AlphaMissense predicts likely pathogenic (score 0.9913) — an in-silico prediction, not a clinical call.

IGF2 p.Cys33Arg

c.97T>C · rs1057518115 · VCV372980

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9913 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9913	likely pathogenic ✓ concordant with ClinVar · top 4% in IGF2
REVEL	0.961	strongly pathogenic-leaning
SaProt	LLR -11.70	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.6, phastCons 1
Regional constraint	o/e 0.38	unconstrained · MANE · 1,851 bp · p 3.2e-08 · regional, not allelic
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: IGF2
Protein: p.Cys33Arg
Coding: c.97T>C
MANE Select: NM_000612
dbSNP: rs1057518115
Type: single nucleotide variant
Location: chr11:2135427 (GRCh38)
Gene constraint: LOEUF 0.496 · pLI 0.96 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 58.95 · 16 PDB
Residue 33: a disulfide bond; 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.Cys33= Likely benign ★★ same residue
IGF2 p.Gln33Ter Conflicting classifications of pathogenicity ★ ⚠ same residue
IGF2 c.157+5G>A Pathogenic ★★ same type
IGF2 p.Glu36Ter Pathogenic/Likely pathogenic ★★ same type
IGF2 p.Gly34Cys Likely pathogenic ★★ same type
IGF2 p.Ser20Ter Likely pathogenic ★★ same type
IGF2 p.Ala167Ser Uncertain significance ★★ ⚠ same type
IGF2 p.Arg138Trp 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-cys33arg (accessed [today's date]).

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