IGF1 p.Ser45=
c.135T>A · rs1880979728 · VCV2643245
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -14 | GERP -3.7 |
| Overall | ||
| CADD | 0.026 | PHRED · no single calibrated threshold — expert panels disagree |
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
- IGF1
- Protein
- p.Ser45=
- Coding
- c.135T>A
- MANE Select
- NM_000618
- dbSNP
- rs1880979728
- Type
- single nucleotide variant
- Location
- chr12:102475728 (GRCh38)
- Gene constraint
- LOEUF 0.675 · pLI 0.76 (gnomAD)
- Structure
- AlphaFold pLDDT 59.69 · 32 PDB
- Residue 45
- a β-strand
Similar variants
- IGF1 p.Ser45Pro Uncertain significance ★ ⚠ same residue
- IGF1 c.*260A>T Uncertain significance ★★ same type
- IGF1 p.Ala115Val Uncertain significance ★★ ⚠ same type
- IGF1 p.Arg119His Uncertain significance ★★ ⚠ same type
- IGF1 p.Arg122His Uncertain significance ★★ ⚠ same type
- IGF1 p.Cys54Trp Uncertain significance ★★ ⚠ same type
- IGF1 p.Leu7Phe Uncertain significance ★★ ⚠ same type
- IGF1 c.402+1663C>A Likely benign ★★ 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/igf1-p-ser45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown