IGF1R p.Pro652=
c.1956T>G · rs45598332 · VCV282974
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.3%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -4 |
| Overall | ||
| CADD | 0.275 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.3%
African / African-American · 225/75,026 alleles
Filtering AF
0.268%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.255%
Overall
0.0149%
240/1,614,150 alleles · rare
exomes 118/1,461,876 · genomes 122/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.3% | 333 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,945 |
| Admixed American | 0.01% | 10,003 |
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
- IGF1R
- Protein
- p.Pro652=
- Coding
- c.1956T>G
- MANE Select
- NM_000875
- dbSNP
- rs45598332
- Type
- single nucleotide variant
- Location
- chr15:98916091 (GRCh38)
- Gene constraint
- LOEUF 0.393 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.54 · 46 PDB
- Residue 652
- an α-helix; the fibronectin type-iii 2 domain
Similar variants
- IGF1R p.Pro652Thr Uncertain significance ★★ ⚠ same residue
- IGF1R c.3187-2A>T Likely pathogenic ★★ same type
- IGF1R c.3457+1G>A Pathogenic/Likely pathogenic ★★ same type
- IGF1R c.641-2A>G Pathogenic ★★ same type
- IGF1R p.Arg365Ter Pathogenic/Likely pathogenic ★★ same type
- IGF1R p.Arg753Ter Pathogenic/Likely pathogenic ★★ same type
- IGF1R p.Cys307Ter Pathogenic ★★ same type
- IGF1R p.Gly1152Arg Pathogenic/Likely 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/igf1r-p-pro652 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown