IGFALS p.Leu79=
c.235C>T · VCV4927391
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0692%, 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 7.4 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 6.191 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0692%
South Asian · 63/90,986 alleles
Filtering AF
0.0554%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0506%
Overall
0.00459%
74/1,611,110 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0692% | 1,444 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,243 |
| European (non-Finnish) | 8.48e-05% | 1,179,720 |
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
- IGFALS
- Protein
- p.Leu79=
- Coding
- c.235C>T
- MANE Select
- NM_004970
- Type
- single nucleotide variant
- Location
- chr16:1792183 (GRCh38)
- Gene constraint
- LOEUF 1.908 · pLI 0.07 (gnomAD)
- Structure
- AlphaFold pLDDT 91.13 · 1 PDB
Similar variants
- IGFALS p.Asn276Ser Likely pathogenic ★★ same type
- IGFALS p.Ala147Thr Uncertain significance ★★ ⚠ same type
- IGFALS p.Ala229Thr Uncertain significance ★★ ⚠ same type
- IGFALS p.Ala258Val Uncertain significance ★★ ⚠ same type
- IGFALS p.Ala551Thr Uncertain significance ★★ ⚠ same type
- IGFALS p.Arg157His Uncertain significance ★★ ⚠ same type
- IGFALS p.Arg306Gln Uncertain significance ★★ ⚠ same type
- IGFALS p.Arg308His 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/igfals-p-leu79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown