Is UBTF p.Leu362= (c.1086C>T) pathogenic?

UBTF p.Leu362= (c.1086C>T) is classified Benign in UBTF (ClinVar, Multiple submitters, 3 submitters; last evaluated 2021-05-05). Common (popmax 17.4%, afr) — too common for a highly-penetrant pathogenic allele.

UBTF p.Leu362=

Q: How common is UBTF p.Leu362= (c.1086C>T) in the general population?

UBTF p.Leu362= (c.1086C>T) is common (popmax 17.4%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1086C>T · rs2228196 · VCV1268482

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 17.4%, afr) — too common for a highly-penetrant pathogenic allele

⚠ 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 -3.5	GERP -4.2
Overall
CADD	2.1	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 17.4% African / African-American · 13,021/75,014 alleles

Filtering AF 17.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 17%

Overall 0.943% 15,214/1,614,156 alleles · common exomes 7,622/1,461,868 · genomes 7,592/152,288 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	17.4%	6
Admixed American	1.23%	81
Remaining individualsnot grpmax-eligible	1.16%	86
Middle Eastern	1.02%	98
Ashkenazi Jewishnot grpmax-eligible	0.206%	485
European (non-Finnish)	0.0475%	2,107
South Asian	0.0351%	2,846
Finnishnot grpmax-eligible	0.0141%	7,115

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.Leu362=
Coding: c.1086C>T
MANE Select: NM_014233
dbSNP: rs2228196
Type: single nucleotide variant
Location: chr17:44211293 (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-leu362 (accessed [today's date]).

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