Is FBP1 p.Ser47= (c.141G>C) pathogenic?

FBP1 p.Ser47= (c.141G>C) is classified Benign/Likely benign in FBP1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-08-21). Ultra-rare (popmax 0.0614%, afr); Associated with fructose-1,6-bisphosphatase deficiency.

What condition is associated with FBP1 p.Ser47= (c.141G>C)?

FBP1 p.Ser47= (c.141G>C) is associated with fructose-1,6-bisphosphatase deficiency (ClinVar).

How common is FBP1 p.Ser47= (c.141G>C) in the general population?

FBP1 p.Ser47= (c.141G>C) is ultra-rare (popmax 0.0614%, afr) (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.Ser47=

c.141G>C · rs148976582 · VCV137362

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0614%, afr)

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	<0.2	all four deltas below 0.2 · C>T here scores Δ0.23 · evaluated, not missing
Constraint at this position
Conservation	phyloP -10	GERP -4.5
Overall
CADD	1.24	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0614% African / African-American · 46/74,906 alleles

Filtering AF 0.0472% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0423%

Overall 0.0043% 69/1,605,190 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0614%	1,628
Admixed American	0.00679%	14,724
East Asian	0.00225%	44,384
Remaining individualsnot grpmax-eligible	0.00161%	62,068
European (non-Finnish)	0.00145%	69,185

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.Ser47=
Coding: c.141G>C
MANE Select: NM_000507
dbSNP: rs148976582
Type: single nucleotide variant
Location: chr9:94639170 (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 47: an α-helix

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-ser47 (accessed [today's date]).

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