GEN1 p.Ile60=
c.180C>A · rs1007053153 · VCV1149345
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00113%, 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 1.5 | GERP -2.2, phastCons 1 |
| Overall | ||
| CADD | 7.619 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00113%
South Asian · 1/88,166 alleles
Overall
6.3e-05%
1/1,587,488 alleles · very rare
exomes 1/1,435,416 · genomes 0/152,072 · joint denominator
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
- GEN1
- Protein
- p.Ile60=
- Coding
- c.180C>A
- MANE Select
- NM_001130009
- dbSNP
- rs1007053153
- Type
- single nucleotide variant
- Location
- chr2:17761414 (GRCh38)
- Gene constraint
- LOEUF 1.422 · pLI <0.01 · ClinGen HI dosage-sensitivity unlikely (gnomAD)
- Structure
- AlphaFold pLDDT 61.79 · 1 PDB
- Residue 60
- the 'xpg-n domain' region; an α-helix
Similar variants
- GEN1 p.Ile60Phe Uncertain significance ★★ ⚠ same residue
- GEN1 p.Ile60Val Uncertain significance ★★ ⚠ same residue
- GEN1 p.Ile60Ser Uncertain significance ★ ⚠ same residue
- GEN1 c.1264+1G>T Uncertain significance ★★ same type
- GEN1 c.953+4A>G Uncertain significance ★★ same type
- GEN1 p.Ala135Ser Uncertain significance ★★ ⚠ same type
- GEN1 p.Ala197Thr Uncertain significance ★★ ⚠ same type
- GEN1 p.Ala320Pro 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/gen1-p-ile60 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown