Is UBTF p.Asp696= (c.2088T>C) pathogenic?

UBTF p.Asp696= (c.2088T>C) is classified Likely benign in UBTF (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-16). Very rare (popmax 0.005%, amr).

How common is UBTF p.Asp696= (c.2088T>C) in the general population?

UBTF p.Asp696= (c.2088T>C) is very rare (popmax 0.005%, amr) (gnomAD).

UBTF p.Asp696=

c.2088T>C · VCV4535497

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.252	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -7.7	GERP -4.4
Overall
CADD	0.998	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% Admixed American · 3/59,966 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000668%

Overall 0.000186% 3/1,613,566 alleles · very rare exomes 2/1,461,880 · genomes 1/151,686 · 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.Asp696=
Coding: c.2088T>C
MANE Select: NM_014233
Type: single nucleotide variant
Location: chr17:44207535 (GRCh38)
Gene constraint: LOEUF 0.133 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 78.52 · 4 PDB
Residue 696: the 'disordered' region

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

Similar variants

UBTF c.59-143C>T Benign ★★ same type
UBTF p.Arg218Gln Uncertain significance ★ ⚠ same type
UBTF p.Asp738Asn Uncertain significance ★ ⚠ same type
UBTF p.Gly479Ser Uncertain significance ★ ⚠ same type
UBTF p.Lys616Arg Uncertain significance ★ ⚠ same type
UBTF p.Met27Ile Uncertain significance ★ ⚠ same type
UBTF p.Leu618= Likely benign ★ same type
UBTF p.Ser758= Likely benign ★ 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/ubtf-p-asp696 (accessed [today's date]).

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