ACTB p.Lys50Asn
c.150G>C · VCV3336993
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.9988 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
2/2 damaging
AlphaMissense, SaProt · REVEL no call
Computational evidence
| Protein change | ||
| AlphaMissense | 0.9988 | likely pathogenic ✓ concordant with ClinVar |
|---|---|---|
| REVEL | 0.6 | indeterminate |
| SaProt | LLR -15.56 | damaging |
| ⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -1.5, phastCons 1 |
| Regional constraint | o/e 0.12 | constrained · MANE · 289 bp · p 4.5e-15 · regional, not allelic |
| Overall | ||
| CADD | 25.9 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
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
- ACTB
- Protein
- p.Lys50Asn
- Coding
- c.150G>C
- MANE Select
- NM_001101
- Type
- single nucleotide variant
- Location
- chr7:5529374 (GRCh38)
- Gene constraint
- LOEUF 0.193 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 95.31 · 93 PDB
- Residue 50
- a cross-link site
Similar variants
- ACTB p.Lys50= Likely benign ★ same residue
- ACTB p.Ala22Thr Likely pathogenic ★★ same type
- ACTB p.Ala7Thr Likely pathogenic ★★ same type
- ACTB p.Arg147Cys Pathogenic ★★ same type
- ACTB p.Arg183Trp Pathogenic ★★ same type
- ACTB p.Arg196Cys Pathogenic ★★ same type
- ACTB p.Arg196His Pathogenic ★★ same type
- ACTB p.Arg196Leu 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/actb-p-lys50asn (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown