Is FBP1 p.Val115= (c.345G>A) pathogenic?

FBP1 p.Val115= (c.345G>A) is classified Benign/Likely benign in FBP1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-25). Rare (popmax 0.253%, afr); Associated with fructose-1,6-bisphosphatase deficiency.

What condition is associated with FBP1 p.Val115= (c.345G>A)?

FBP1 p.Val115= (c.345G>A) is associated with fructose-1,6-bisphosphatase deficiency (ClinVar).

How common is FBP1 p.Val115= (c.345G>A) in the general population?

FBP1 p.Val115= (c.345G>A) is rare (popmax 0.253%, 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.Val115=

c.345G>A · rs61753273 · VCV377874

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.253%, 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	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.53	GERP 0.88, phastCons 0.99
Overall
CADD	7.165	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.253% African / African-American · 190/74,968 alleles

Filtering AF 0.224% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.213%

Overall 0.0141% 227/1,612,330 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.253%	395
Remaining individualsnot grpmax-eligible	0.0368%	2,716
Middle Eastern	0.0165%	6,060
Admixed American	0.0117%	8,574
South Asian	0.00549%	18,210
European (non-Finnish)	8.49e-05%	1,178,507

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.Val115=
Coding: c.345G>A
MANE Select: NM_000507
dbSNP: rs61753273
Type: single nucleotide variant
Location: chr9:94617849 (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 115: 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 p.Val115fs Pathogenic ★ same residue
FBP1 p.Val115Gly Likely pathogenic ★ same residue
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

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-val115 (accessed [today's date]).

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