Is UBTF p.Lys455= (c.1365G>A) pathogenic?

UBTF p.Lys455= (c.1365G>A) is classified Likely benign in UBTF (ClinVar, Single submitter, 2 submitters; last evaluated 2024-07-19). Rare (popmax 0.906%, afr).

How common is UBTF p.Lys455= (c.1365G>A) in the general population?

UBTF p.Lys455= (c.1365G>A) is rare (popmax 0.906%, afr) (gnomAD).

UBTF p.Lys455=

c.1365G>A · rs34269581 · VCV3050205

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.906%, afr)

⚠ 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 1.7	GERP -1.2, phastCons 1
Overall
CADD	10.15	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.906% African / African-American · 678/74,808 alleles

Filtering AF 0.85% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.827%

Overall 0.0474% 762/1,606,768 alleles · rare exomes 348/1,454,470 · genomes 414/152,298 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.906%	110
Admixed American	0.0628%	1,594
Remaining individualsnot grpmax-eligible	0.0547%	1,829
Middle Eastern	0.0511%	1,955
South Asian	0.0022%	45,395
European (non-Finnish)	0.000679%	147,305

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.Lys455=
Coding: c.1365G>A
MANE Select: NM_014233
dbSNP: rs34269581
Type: single nucleotide variant
Location: chr17:44210468 (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-lys455 (accessed [today's date]).

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