ERCC8 p.Arg25=
c.75G>A · rs755656702 · VCV1905442
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.025 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.96 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -0.86 | GERP -3.5, phastCons 0.003 |
| Overall | ||
| CADD | 13.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,082 alleles
Filtering AF
0.00514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00375%
Overall
0.000682%
11/1,613,302 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,082 |
| South Asian | 0.00988% | 10,118 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,472 |
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
- ERCC8
- Protein
- p.Arg25=
- Coding
- c.75G>A
- MANE Select
- NM_000082
- dbSNP
- rs755656702
- Type
- single nucleotide variant
- Location
- chr5:60944934 (GRCh38)
- Gene constraint
- LOEUF 1.608 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.72 · 16 PDB
- Residue 25
- an α-helix
Similar variants
- ERCC8 c.1041+1G>T Pathogenic/Likely pathogenic ★★ same type
- ERCC8 c.1042-2A>G Pathogenic/Likely pathogenic ★★ same type
- ERCC8 c.173+1119G>C Pathogenic/Likely pathogenic ★★ same type
- ERCC8 c.173+1G>A Pathogenic/Likely pathogenic ★★ same type
- ERCC8 c.275+1G>A Pathogenic ★★ same type
- ERCC8 c.276-1G>A Likely pathogenic ★★ same type
- ERCC8 c.399+1G>A Likely pathogenic ★★ same type
- ERCC8 c.551-1G>A 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/ercc8-p-arg25 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown