Is FBP1 p.Ser321fs (c.960del) pathogenic?

FBP1 p.Ser321fs (c.960del) is classified Pathogenic in FBP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-16). No gnomAD frequency available for this variant; Associated with fructose-1,6-bisphosphatase deficiency.

What condition is associated with FBP1 p.Ser321fs (c.960del)?

FBP1 p.Ser321fs (c.960del) is associated with fructose-1,6-bisphosphatase deficiency (ClinVar).

How common is FBP1 p.Ser321fs (c.960del) in the general population?

FBP1 p.Ser321fs (c.960del) is no gnomAD frequency available for this variant (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.Ser321fs

c.960del · rs2538927195 · VCV2797845

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

fructose-1,6-bisphosphatase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (7 of 7) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: FBP1
Protein: p.Ser321fs
Coding: c.960del
MANE Select: NM_000507
dbSNP: rs2538927195
Type: Deletion
Location: chr9:94603438 (GRCh38)
Gene constraint: LOEUF 1.156 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 94.46 · 51 PDB

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.Lys204fs Pathogenic/Likely pathogenic ★★ same condition
FBP1 p.Pro235fs Pathogenic/Likely pathogenic ★★ same condition
FBP1 p.Val131fs Pathogenic ★★ same condition
FBP1 p.Ala44fs Pathogenic ★ same condition
FBP1 p.Gly260fs Pathogenic ★ same condition
FBP1 p.Ile195fs Pathogenic ★ same condition
FBP1 p.Leu95fs Pathogenic ★ same condition
FBP1 p.Met1fs 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-ser321fs (accessed [today's date]).

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