IGF2R p.Pro722=
c.2166G>A · VCV3772328
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0351%, 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 -11 | GERP -3.4 |
| Overall | ||
| CADD | 0.107 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0351%
South Asian · 32/91,056 alleles
Filtering AF
0.0256%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0222%
Overall
0.0026%
42/1,613,088 alleles · ultra-rare
exomes 42/1,460,742 · genomes 0/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0351% | 2,846 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,812 |
| European (non-Finnish) | 0.00017% | 589,946 |
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
- IGF2R
- Protein
- p.Pro722=
- Coding
- c.2166G>A
- MANE Select
- NM_000876
- Type
- single nucleotide variant
- Location
- chr6:160047273 (GRCh38)
- Gene constraint
- LOEUF 0.421 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 73.48 · 24 PDB
- Residue 722
- the mrh 5 domain
Similar variants
- IGF2R p.Asp2219= Benign/Likely benign ★★ same type
- IGF2R p.Leu817Val Benign ★★ same type
- IGF2R p.Pro2129= Benign/Likely benign ★★ same type
- IGF2R p.His151Tyr Likely pathogenic ★ ⚠ same type
- IGF2R c.289+2T>C Uncertain significance ★ same type
- IGF2R p.Ala1033Pro Uncertain significance ★ ⚠ same type
- IGF2R p.Ala104Thr Uncertain significance ★ ⚠ same type
- IGF2R p.Ala1252Thr 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/igf2r-p-pro722 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown