ERCC6 p.Asp98=
c.294C>T · rs780795428 · VCV1084520
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0312%, eas)
Conditions
1
Inborn genetic diseases
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 -5 | GERP -3.9 |
| Overall | ||
| CADD | 0.695 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0312%
East Asian · 14/44,882 alleles
Filtering AF
0.0188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0151%
Overall
0.00155%
25/1,614,012 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0312% | 3,206 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| South Asian | 0.0022% | 45,543 |
| African / African-American | 0.00134% | 74,886 |
| European (non-Finnish) | 0.000424% | 236,009 |
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
- ERCC6
- Protein
- p.Asp98=
- Coding
- c.294C>T
- MANE Select
- NM_000124
- dbSNP
- rs780795428
- Type
- single nucleotide variant
- Location
- chr10:49532671 (GRCh38)
- Gene constraint
- LOEUF 0.803 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.12 · 12 PDB
- Residue 98
- the 'n-terminal domain; essential for its chromatin remodeling activity' region
Similar variants
- ERCC6 c.1397+1G>C Likely pathogenic ★★ same condition
- ERCC6 p.Arg176Ter Pathogenic ★★ same condition
- ERCC6 p.Arg612Ter Pathogenic/Likely pathogenic ★★ same condition
- ERCC6 p.Arg857Ter Pathogenic ★★ same condition
- ERCC6 p.Gln723Ter Pathogenic/Likely pathogenic ★★ same condition
- ERCC6 p.Ser687Leu Pathogenic ★★ same condition
- ERCC6 p.Ala1075Thr Uncertain significance ★★ ⚠ same condition
- ERCC6 p.Ala1167Asp Uncertain significance ★★ ⚠ same condition
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/ercc6-p-asp98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown