Is UBAP1 p.Asp99fs (c.295dup) pathogenic?

UBAP1 p.Asp99fs (c.295dup) is classified Pathogenic in UBAP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-10). No gnomAD frequency available for this variant; Associated with spastic paraplegia 80, autosomal dominant.

What condition is associated with UBAP1 p.Asp99fs (c.295dup)?

UBAP1 p.Asp99fs (c.295dup) is associated with spastic paraplegia 80, autosomal dominant (ClinVar).

How common is UBAP1 p.Asp99fs (c.295dup) in the general population?

UBAP1 p.Asp99fs (c.295dup) is no gnomAD frequency available for this variant (gnomAD).

How is Autosomal dominant spastic paraplegia type 80 inherited?

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

UBAP1 p.Asp99fs

c.295dup · rs1563920000 · VCV627555

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

spastic paraplegia 80, autosomal dominant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 4 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -4.3	GERP -3.8

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: UBAP1
Protein: p.Asp99fs
Coding: c.295dup
MANE Select: NM_016525
dbSNP: rs1563920000
Type: Duplication
Location: chr9:34241319 (GRCh38)
Gene constraint: LOEUF 0.285 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.60 · 3 PDB
Residue 99: the 'disordered' region

Full UBAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

spastic paraplegia 80, autosomal dominant — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal dominant spastic paraplegia type 80 (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Childhood

Similar variants

UBAP1 p.Val144fs Likely pathogenic ★ same condition
UBAP1 p.Cys161fs Likely pathogenic same condition
UBAP1 p.Glu97fs Pathogenic same condition
UBAP1 p.Leu121fs Pathogenic same condition
UBAP1 p.Lys143fs Pathogenic ★★ same condition
UBAP1 p.Glu455fs Uncertain significance ★★ same condition
UBAP1 c.-20C>T Likely pathogenic ★ same condition
UBAP1 p.Asp158_Phe159insTer 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/ubap1-p-asp99fs (accessed [today's date]).

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