Is UBTF p.Asp687= (c.2061C>T) pathogenic?

UBTF p.Asp687= (c.2061C>T) is classified Likely benign in UBTF (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-05). Ultra-rare (popmax 0.0504%, nfe).

How common is UBTF p.Asp687= (c.2061C>T) in the general population?

UBTF p.Asp687= (c.2061C>T) is ultra-rare (popmax 0.0504%, nfe) (gnomAD).

UBTF p.Asp687=

c.2061C>T · rs142426190 · VCV2647822

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0504%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.255	benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -9.3	GERP -4.8
Overall
CADD	1.392	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0504% European (non-Finnish) · 595/1,180,006 alleles

Filtering AF 0.047% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0457%

Overall 0.0388% 627/1,613,928 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0504%	1,983
Remaining individualsnot grpmax-eligible	0.0224%	4,463
Middle Eastern	0.0164%	6,084
African / African-American	0.0147%	6,807
South Asian	0.00549%	18,214
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,600

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.Asp687=
Coding: c.2061C>T
MANE Select: NM_014233
dbSNP: rs142426190
Type: single nucleotide variant
Location: chr17:44207562 (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-asp687 (accessed [today's date]).

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