FBP1 p.Ala103=
c.309C>A · rs746720956 · VCV725525
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, 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 3.9 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 7.294 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,010 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000124%
2/1,614,068 alleles · very rare
exomes 1/1,461,876 · genomes 1/152,192 · 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
- FBP1
- Protein
- p.Ala103=
- Coding
- c.309C>A
- MANE Select
- NM_000507
- dbSNP
- rs746720956
- Type
- single nucleotide variant
- Location
- chr9:94620353 (GRCh38)
- Gene constraint
- LOEUF 1.156 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 94.46 · 51 PDB
Similar variants
- FBP1 p.Ala103Thr Uncertain significance ★ ⚠ same residue
- FBP1 c.426+1G>A Pathogenic ★★ same type
- FBP1 c.427-2A>G Likely pathogenic ★★ same type
- FBP1 p.Arg158Trp Pathogenic ★★ same type
- FBP1 p.Asp119Asn Pathogenic/Likely pathogenic ★★ same type
- FBP1 p.Glu281Lys Pathogenic/Likely pathogenic ★★ same type
- FBP1 p.Glu281Ter Pathogenic ★★ same type
- FBP1 p.Gly164Ser 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/fbp1-p-ala103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown