Is UBTF p.Asp697del (c.2088TGA[1]) pathogenic?

UBTF p.Asp697del (c.2088TGA[1]) is classified Uncertain significance in UBTF (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-18). Very rare (popmax 8.47e-05%, nfe).

How common is UBTF p.Asp697del (c.2088TGA[1]) in the general population?

UBTF p.Asp697del (c.2088TGA[1]) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

UBTF p.Asp697del

c.2088TGA[1] · VCV3365492

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.34	GERP -2.9, phastCons 0.96
Region caveats
Repeat context	tandem	(TCCTCA)n simple repeat · ambiguous alignment · confidence, not pathogenicity

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,026 alleles

Overall 6.2e-05% 1/1,614,096 alleles · very rare exomes 1/1,461,872 · genomes 0/152,224 · joint denominator

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: UBTF
Protein: p.Asp697del
Coding: c.2088TGA[1]
MANE Select: NM_014233
Type: Microsatellite
Location: chr17:44207530 (GRCh38)

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

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/ubtf-p-asp697del (accessed [today's date]).

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