THRAP3 p.Arg347=
c.1041G>A · rs371208940 · VCV3177130
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0519%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.6 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 13.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0519%
Admixed American · 26/50,050 alleles
Filtering AF
0.0364%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0311%
Overall
0.0206%
323/1,567,536 alleles · ultra-rare
exomes 294/1,415,484 · genomes 29/152,052 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0519% | 1,925 |
| Remaining individualsnot grpmax-eligible | 0.0299% | 3,348 |
| European (non-Finnish) | 0.0233% | 4,284 |
| African / African-American | 0.00967% | 10,341 |
| Finnishnot grpmax-eligible | 0.0016% | 62,480 |
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
- THRAP3
- Protein
- p.Arg347=
- Coding
- c.1041G>A
- MANE Select
- NM_005119
- dbSNP
- rs371208940
- Type
- single nucleotide variant
- Location
- chr1:36289060 (GRCh38)
- Gene constraint
- LOEUF 0.244 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.40
- Residue 347
- the 'disordered' region
Similar variants
- THRAP3 c.2647-17A>G Likely benign ★★ same type
- THRAP3 p.Ala117Ser Uncertain significance ★ ⚠ same type
- THRAP3 p.Ala236Val Uncertain significance ★ ⚠ same type
- THRAP3 p.Ala291Val Uncertain significance ★ ⚠ same type
- THRAP3 p.Ala581Thr Uncertain significance ★ ⚠ same type
- THRAP3 p.Arg153Gln Uncertain significance ★ ⚠ same type
- THRAP3 p.Arg156His Uncertain significance ★ ⚠ same type
- THRAP3 p.Arg15Cys 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/thrap3-p-arg347 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown