TRIO p.Pro11=
c.33C>T · rs1013676539 · VCV1200872
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00801%, nfe)
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 2.1 | GERP -0.41, phastCons 1 |
| Overall | ||
| CADD | 13.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
European (non-Finnish) · 67/836,476 alleles
Filtering AF
0.0064%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00582%
Overall
0.00695%
69/992,760 alleles · very rare
exomes 50/846,682 · genomes 19/146,078 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00801% | 12,485 |
| Admixed American | 0.00617% | 16,208 |
| Remaining individualsnot grpmax-eligible | 0.00331% | 30,198 |
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
- TRIO
- Protein
- p.Pro11=
- Coding
- c.33C>T
- MANE Select
- NM_007118
- dbSNP
- rs1013676539
- Type
- single nucleotide variant
- Location
- chr5:14143758 (GRCh38)
- Gene constraint
- LOEUF 0.217 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Similar variants
- TRIO c.2391+1G>A Pathogenic/Likely pathogenic ★★ same type
- TRIO c.3447+2T>C Likely pathogenic ★★ same type
- TRIO c.5497-1G>C Likely pathogenic ★★ same type
- TRIO c.6153+1G>A Pathogenic/Likely pathogenic ★★ same type
- TRIO p.Arg1078Gln Pathogenic/Likely pathogenic ★★ same type
- TRIO p.Arg1078Trp Pathogenic/Likely pathogenic ★★ same type
- TRIO p.Arg1411Ter Pathogenic/Likely pathogenic ★★ same type
- TRIO p.Arg1428Gln 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/trio-p-pro11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown