ACTC1 p.Glu239Ter
c.715G>T · rs1555418785 · VCV1678008
Uncertain significance
Single submitter
Classification
Uncertain significance
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 carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 5 of 7 |
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.34 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.3, phastCons 1 |
| Overall | ||
| CADD | 47.0 | 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
- ACTC1
- Protein
- p.Glu239Ter
- Coding
- c.715G>T
- MANE Select
- NM_005159
- dbSNP
- rs1555418785
- Type
- single nucleotide variant
- Location
- chr15:34792183 (GRCh38)
- Gene constraint
- LOEUF 0.511 · pLI 0.97 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 95.47 · 16 PDB
Similar variants
- ACTC1 p.Glu239Gln Likely pathogenic ★ same residue
- ACTC1 p.Glu239Val Likely pathogenic ★ same residue
- ACTC1 p.Glu101Lys Pathogenic ★★★ same type
- ACTC1 p.Gly345Val Uncertain significance ★★★ ⚠ same type
- ACTC1 p.Pro266Leu Uncertain significance ★★★ ⚠ same type
- ACTC1 p.Val56Ile Uncertain significance ★★★ ⚠ same type
- ACTC1 p.Ala297Ser Pathogenic ★★ ⚠ same type
- ACTC1 p.Gly247Asp 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/actc1-p-glu239ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown