DNA2 p.Asn889fs
c.2664del · rs2493902309 · VCV2193390
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 17 of 21 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 3.4 | GERP 1.2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- DNA2
- Protein
- p.Asn889fs
- Coding
- c.2664del
- MANE Select
- NM_001080449
- dbSNP
- rs2493902309
- Type
- Deletion
- Location
- chr10:68422258 (GRCh38)
- Gene constraint
- LOEUF 1.115 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.82 · 1 PDB
- Residue 889
- the upf1-type sf1b helicase c-terminal domain; the 'helicase activity' region
Similar variants
- DNA2 p.Asn889Ser Uncertain significance ★ ⚠ same residue
- DNA2 c.73_74+10del Likely pathogenic ★★ same type
- DNA2 p.Asn463fs Uncertain significance ★★ same type
- DNA2 p.Cys415fs Uncertain significance ★★ same type
- DNA2 p.Leu1054fs Uncertain significance ★★ same type
- DNA2 p.Ser725_Leu726insTer Uncertain significance ★★ same type
- DNA2 p.Ser779fs Uncertain significance ★★ same type
- DNA2 p.Val418_Pro419del 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/dna2-p-asn889fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown