ERCC6 p.Ser1062=
c.3186T>C · rs35365613 · VCV300053
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.45%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.22 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.52 | GERP -4 |
| Overall | ||
| CADD | 0.794 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.45%
East Asian · 650/44,882 alleles
Filtering AF
1.36%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.32%
Overall
0.0558%
900/1,614,176 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.45% | 69 |
| Remaining individualsnot grpmax-eligible | 0.0768% | 1,302 |
| Admixed American | 0.0766% | 1,305 |
| South Asian | 0.0242% | 4,140 |
| Middle Eastern | 0.0165% | 6,062 |
| European (non-Finnish) | 0.0109% | 9,148 |
| Finnishnot grpmax-eligible | 0.00469% | 21,337 |
| African / African-American | 0.00133% | 75,056 |
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.Ser1062=
- Coding
- c.3186T>C
- MANE Select
- NM_000124
- dbSNP
- rs35365613
- Type
- single nucleotide variant
- Location
- chr10:49470774 (GRCh38)
- Gene constraint
- LOEUF 0.803 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.12 · 12 PDB
- Residue 1062
- the 'disordered' region
Similar variants
- ERCC6 c.1397+1G>C Likely pathogenic ★★ same type
- ERCC6 c.1526+1G>T Pathogenic/Likely pathogenic ★★ same type
- ERCC6 c.2169+1G>A Likely pathogenic ★★ same type
- ERCC6 c.2170-1G>A Pathogenic/Likely pathogenic ★★ same type
- ERCC6 c.2286+1G>A Pathogenic/Likely pathogenic ★★ same type
- ERCC6 c.2287-2A>G Pathogenic/Likely pathogenic ★★ same type
- ERCC6 c.2599-26A>G Pathogenic/Likely pathogenic ★★ same type
- ERCC6 c.2709+1G>T Pathogenic/Likely pathogenic ★★ 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/ercc6-p-ser1062 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown