Is FBP1 p.Ala302= (c.906C>T) pathogenic?

FBP1 p.Ala302= (c.906C>T) is classified Conflicting classifications of pathogenicity in FBP1 (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2026-01-26). Rare (popmax 0.919%, sas); Associated with fructose-1,6-bisphosphatase deficiency.

What condition is associated with FBP1 p.Ala302= (c.906C>T)?

FBP1 p.Ala302= (c.906C>T) is associated with fructose-1,6-bisphosphatase deficiency (ClinVar).

How common is FBP1 p.Ala302= (c.906C>T) in the general population?

FBP1 p.Ala302= (c.906C>T) is rare (popmax 0.919%, sas) (gnomAD).

How is Fructose-1,6-bisphosphatase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

FBP1 p.Ala302=

c.906C>T · rs28369776 · VCV377876

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.919%, sas)

Conditions

fructose-1,6-bisphosphatase deficiency

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 -1.8	GERP -3.7
Overall
CADD	0.726	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.919% South Asian · 837/91,064 alleles

Filtering AF 0.867% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.847%

Overall 0.0711% 1,148/1,614,054 alleles · rare exomes 1,060/1,461,832 · genomes 88/152,222 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.919%	109
Ashkenazi Jewishnot grpmax-eligible	0.324%	308
Middle Eastern	0.198%	505
Remaining individualsnot grpmax-eligible	0.08%	1,250
African / African-American	0.0213%	4,689
Admixed American	0.0183%	5,456
European (non-Finnish)	0.0106%	9,440
East Asian	0.00223%	44,872

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.Ala302=
Coding: c.906C>T
MANE Select: NM_000507
dbSNP: rs28369776
Type: single nucleotide variant
Location: chr9:94603492 (GRCh38)
Gene constraint: LOEUF 1.156 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 94.46 · 51 PDB
Residue 302: a β-strand

Full FBP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

fructose-1,6-bisphosphatase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Fructose-1,6-bisphosphatase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages
Prevalence: 1-9 / 1 000 000 (Italy)

Similar variants

FBP1 c.426+1G>A Pathogenic ★★ same condition
FBP1 c.427-2A>G Likely pathogenic ★★ same condition
FBP1 p.Arg158Trp Pathogenic ★★ same condition
FBP1 p.Asp119Asn Pathogenic/Likely pathogenic ★★ same condition
FBP1 p.Glu281Lys Pathogenic/Likely pathogenic ★★ same condition
FBP1 p.Glu281Ter Pathogenic ★★ same condition
FBP1 p.Gly164Ser Pathogenic/Likely pathogenic ★★ ⚠ same condition
FBP1 p.Gly260Arg Pathogenic/Likely pathogenic ★★ same condition

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-ala302 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown