ACTRT2 p.Ser200=
c.600C>T · rs533735087 · VCV3025471
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0383%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | |
| Overall | ||
| CADD | 0.018 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0383%
Admixed American · 23/60,012 alleles
Filtering AF
0.0261%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0222%
Overall
0.00428%
69/1,612,628 alleles · ultra-rare
exomes 62/1,460,334 · genomes 7/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0383% | 2,609 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0237% | 4,228 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,809 |
| East Asian | 0.00446% | 22,428 |
| African / African-American | 0.00267% | 37,521 |
| European (non-Finnish) | 0.00229% | 43,696 |
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
- ACTRT2
- Protein
- p.Ser200=
- Coding
- c.600C>T
- MANE Select
- NM_080431
- dbSNP
- rs533735087
- Type
- single nucleotide variant
- Location
- chr1:3022286 (GRCh38)
- Gene constraint
- LOEUF 1.307 · pLI 0.29 (gnomAD)
- Structure
- AlphaFold pLDDT 93.42
Similar variants
- ACTRT2 p.Ala135Val Uncertain significance ★ ⚠ same type
- ACTRT2 p.Ala178Thr Uncertain significance ★ ⚠ same type
- ACTRT2 p.Ala224Asp Uncertain significance ★ ⚠ same type
- ACTRT2 p.Ala23Val Uncertain significance ★ ⚠ same type
- ACTRT2 p.Ala259Gly Uncertain significance ★ ⚠ same type
- ACTRT2 p.Ala259Val Uncertain significance ★ ⚠ same type
- ACTRT2 p.Ala323Thr Uncertain significance ★ ⚠ same type
- ACTRT2 p.Ala361Thr 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/actrt2-p-ser200 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown