TRIOBP p.Pro2103=
c.6309G>A · VCV4754914
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0133%, 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 -7.9 | GERP -4.5 |
| Overall | ||
| CADD | 0.069 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0133%
Admixed American · 8/60,004 alleles
Filtering AF
0.00661%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00482%
Overall
0.00192%
31/1,613,050 alleles · ultra-rare
exomes 31/1,460,884 · genomes 0/152,166 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0133% | 7,501 |
| East Asian | 0.00446% | 22,432 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,496 |
| European (non-Finnish) | 0.00153% | 65,551 |
| African / African-American | 0.00133% | 74,998 |
| South Asian | 0.0011% | 91,078 |
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
- TRIOBP
- Protein
- p.Pro2103=
- Coding
- c.6309G>A
- MANE Select
- NM_001039141
- Type
- single nucleotide variant
- Location
- chr22:37759249 (GRCh38)
- Gene constraint
- LOEUF 0.865 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 40.77
Similar variants
- TRIOBP p.Pro2103Leu Uncertain significance ★★ ⚠ same residue
- TRIOBP c.5184+1G>A Pathogenic/Likely pathogenic ★★ same type
- TRIOBP p.Arg1025Ter Pathogenic/Likely pathogenic ★★ same type
- TRIOBP p.Arg1068Ter Pathogenic/Likely pathogenic ★★ same type
- TRIOBP p.Arg1117Ter Pathogenic ★★ same type
- TRIOBP p.Arg1745Ter Likely pathogenic ★★ same type
- TRIOBP p.Arg347Ter Pathogenic ★★ same type
- TRIOBP p.Arg399Ter 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/triobp-p-pro2103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown