TPI1 p.Phe103=
c.309T>C · rs11548749 · VCV2799109
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
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 -0.052 | GERP -1.9, phastCons 0.88 |
| Overall | ||
| CADD | 9.694 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/75,026 alleles
Filtering AF
0.000442%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000124%
2/1,614,136 alleles · very rare
exomes 2/1,461,884 · genomes 0/152,252 · joint denominator
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
- TPI1
- Protein
- p.Phe103=
- Coding
- c.309T>C
- MANE Select
- NM_000365
- dbSNP
- rs11548749
- Type
- single nucleotide variant
- Location
- chr12:6869168 (GRCh38)
- Gene constraint
- LOEUF 0.563 · pLI 0.87 (gnomAD)
- Structure
- AlphaFold pLDDT 96.87 · 29 PDB
Similar variants
- TPI1 p.Glu105Asp Pathogenic/Likely pathogenic ★★ same type
- TPI1 c.543+6C>T Uncertain significance ★★ same type
- TPI1 c.-11G>A Uncertain significance ★★ same type
- TPI1 p.Ala200Val Uncertain significance ★★ ⚠ same type
- TPI1 p.Arg206Cys Uncertain significance ★★ ⚠ same type
- TPI1 p.Arg206His Uncertain significance ★★ ⚠ same type
- TPI1 p.Arg53Trp Uncertain significance ★★ ⚠ same type
- TPI1 p.Asn246Ser 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/tpi1-p-phe103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown