Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.83%, eas)
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 -2.9 | GERP -3.2 |
| Overall | ||
| CADD | 0.467 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.83%
East Asian · 823/44,888 alleles
Filtering AF
1.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.69%
Overall
0.0735%
1,186/1,613,712 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.83% | 55 |
| Remaining individualsnot grpmax-eligible | 0.194% | 516 |
| African / African-American | 0.0746% | 1,340 |
| Admixed American | 0.0167% | 6,002 |
| European (non-Finnish) | 0.0146% | 6,861 |
| Finnishnot grpmax-eligible | 0.00313% | 31,987 |
| South Asian | 0.0022% | 45,530 |
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
- ERCC1
- Protein
- p.Ile264=
- Coding
- c.792C>T
- MANE Select
- NM_001983
- dbSNP
- rs3212976
- Type
- single nucleotide variant
- Location
- chr19:45413728 (GRCh38)
- Gene constraint
- LOEUF 1.306 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.48 · 14 PDB
- Residue 264
- the 'hhh2, dimerization with ercc4/xpf' region; an α-helix
Similar variants
- ERCC1 c.526-1G>A Likely pathogenic ★★ same type
- ERCC1 p.Arg41Ter Pathogenic ★★ same type
- ERCC1 c.843+52A>G Uncertain significance ★★ same type
- ERCC1 p.Ala265Thr Uncertain significance ★★ ⚠ same type
- ERCC1 p.Arg156Gln Uncertain significance ★★ ⚠ same type
- ERCC1 p.Arg207Trp Uncertain significance ★★ ⚠ same type
- ERCC1 p.Asn110Ser Uncertain significance ★★ ⚠ same type
- ERCC1 p.Gly85Arg 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/ercc1-p-ile264 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown