KRAS p.Arg164Ter
c.490C>T · rs200186819 · VCV3065766
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 in a LoF-intolerant gene; NMD-escape possible for C-terminal truncations |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.37 | acceptor loss, 39 bp away · masked 0 · deltas |
| Constraint at this position | ||
| Conservation | phyloP 8.7 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 22.6 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Finnishnot grpmax-eligible | 0.00939% | 10,649 |
| South Asiangrpmax | 0.0033% | 30,333 |
| African / African-American | 0.00134% | 74,786 |
| European (non-Finnish) | 0.00017% | 589,036 |
Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- KRAS
- Protein
- p.Arg164Ter
- Coding
- c.490C>T
- MANE Select
- NM_004985 · reported on NM_033360
- dbSNP
- rs200186819
- Type
- single nucleotide variant
- Location
- chr12:25215521 (GRCh38)
- Gene constraint
- LOEUF 0.264 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 91.65 · 549 PDB
- Residue 164
- an α-helix
Similar variants
- KRAS p.Arg164Gln Uncertain significance ★★ same residue
- KRAS p.Arg164= Likely benign ★ same residue
- KRAS p.Asp153Val Pathogenic ★★★ same condition
- KRAS p.Asp30= Likely benign ★★★ same condition
- KRAS p.Val8= Likely benign ★★★ same condition
- KRAS p.Gly12Asp Pathogenic/Likely pathogenic ★★ same condition
- KRAS p.Gly12Val Pathogenic ★★ same condition
- KRAS p.Ala130Val 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/kras-p-arg164ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown