IGF1R p.Val164=
c.492G>T · rs45582234 · VCV2158119
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.196%, afr)
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 0.24 | GERP -0.077, phastCons 0.9 |
| Overall | ||
| CADD | 5.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.196%
African / African-American · 147/75,028 alleles
Filtering AF
0.17%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.16%
Overall
0.0102%
164/1,614,176 alleles · rare
exomes 81/1,461,886 · genomes 83/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.196% | 510 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,814 |
| Admixed American | 0.00833% | 12,007 |
| European (non-Finnish) | 0.000339% | 295,009 |
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.Val164=
- Coding
- c.492G>T
- MANE Select
- NM_000875
- dbSNP
- rs45582234
- Type
- single nucleotide variant
- Location
- chr15:98707959 (GRCh38)
- Gene constraint
- LOEUF 0.393 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.54 · 46 PDB
- Residue 164
- an α-helix
Similar variants
- 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
- IGF1R c.1102+6T>C 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/igf1r-p-val164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown