Is UBAP1 p.Ala111fs (c.327_330dup) pathogenic?

UBAP1 p.Ala111fs (c.327330dup) is classified Likely pathogenic in UBAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-01). Associated with UBAP1-related disorder.

What condition is associated with UBAP1 p.Ala111fs (c.327_330dup)?

UBAP1 p.Ala111fs (c.327_330dup) is associated with UBAP1-related disorder (ClinVar).

UBAP1 p.Ala111fs

c.327_330dup · VCV4902990

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

UBAP1-related disorder

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 5.7	GERP 1.9, phastCons 1

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

Variant & gene context

Gene: UBAP1
Protein: p.Ala111fs
Coding: c.327_330dup
MANE Select: NM_016525
Type: Duplication
Location: chr9:34241351 (GRCh38)
Gene constraint: LOEUF 0.285 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.60 · 3 PDB
Residue 111: the 'disordered' region

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

Disease context

UBAP1-related disorder

Similar variants

UBAP1 p.Leu169Met Conflicting classifications of pathogenicity ★ ⚠ same condition
UBAP1 p.Glu397Lys Benign ⚠ same condition
UBAP1 p.Val144fs Likely pathogenic ★ same type
UBAP1 c.1083+4dup Uncertain significance ★ same type
UBAP1 c.-8+10dup Likely benign ★ same type
UBAP1 p.Asp99fs Pathogenic same type
UBAP1 p.Cys161fs Likely pathogenic same type
UBAP1 p.Glu97fs Pathogenic same type

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-ala111fs (accessed [today's date]).

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