ERCC2 p.Lys82Ter
c.244A>T · rs2514044862 · VCV2760678
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 4 of 23 |
| Splicing | ||
| SpliceAI | Δ0.50 | donor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 52.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ERCC2
- Protein
- p.Lys82Ter
- Coding
- c.244A>T
- MANE Select
- NM_000400
- dbSNP
- rs2514044862
- Type
- single nucleotide variant
- Location
- chr19:45368932 (GRCh38)
- Gene constraint
- LOEUF 1.089 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 87.74 · 55 PDB
- Residue 82
- the helicase atp-binding domain; an α-helix
Similar variants
- MAG p.His82= Benign/Likely benign ★★ same residue
- ERCC2 c.1238-1G>C Likely pathogenic ★★ same type
- ERCC2 c.1308-2A>G Likely pathogenic ★★ same type
- ERCC2 c.1378-1G>T Pathogenic/Likely pathogenic ★★ same type
- ERCC2 c.1479+2T>C Pathogenic/Likely pathogenic ★★ same type
- ERCC2 c.1480-1G>C Pathogenic/Likely pathogenic ★★ same type
- ERCC2 c.1480-2A>C Pathogenic/Likely pathogenic ★★ same type
- ERCC2 c.1544-1G>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/ercc2-p-lys82ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown