IGF2BP2 p.Ile562=
c.1686C>T · VCV4873754
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00988%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.6 | GERP -3.7 |
| Overall | ||
| CADD | 6.664 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00988%
South Asian · 9/91,074 alleles
Filtering AF
0.00514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00375%
Overall
0.000744%
12/1,613,684 alleles · very rare
exomes 10/1,461,344 · genomes 2/152,340 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00988% | 10,119 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,466 |
| African / African-American | 0.00133% | 75,056 |
| European (non-Finnish) | 8.48e-05% | 1,179,586 |
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
- IGF2BP2
- Protein
- p.Ile562=
- Coding
- c.1686C>T
- MANE Select
- NM_006548
- Type
- single nucleotide variant
- Location
- chr3:185647046 (GRCh38)
- Gene constraint
- LOEUF 0.325 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.70 · 4 PDB
- Residue 562
- a β-strand; the kh 4 domain
Similar variants
- IGF2BP2 p.Ile562Thr Uncertain significance ★ ⚠ same residue
- IGF2BP2 p.Ala103Val Uncertain significance ★ ⚠ same type
- IGF2BP2 p.Ala16Thr Uncertain significance ★ ⚠ same type
- IGF2BP2 p.Ala182Thr Uncertain significance ★ ⚠ same type
- IGF2BP2 p.Ala31Glu Uncertain significance ★ ⚠ same type
- IGF2BP2 p.Ala348Thr Uncertain significance ★ ⚠ same type
- IGF2BP2 p.Ala394Val Uncertain significance ★ ⚠ same type
- IGF2BP2 p.Ala441Thr 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/igf2bp2-p-ile562 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown