Is UBTF p.Lys612= (c.1836G>A) pathogenic?

UBTF p.Lys612= (c.1836G>A) is classified Benign in UBTF (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-14). Low-frequency (popmax 2.24%, amr); Associated with UBTF-related disorder.

What condition is associated with UBTF p.Lys612= (c.1836G>A)?

UBTF p.Lys612= (c.1836G>A) is associated with UBTF-related disorder (ClinVar).

How common is UBTF p.Lys612= (c.1836G>A) in the general population?

UBTF p.Lys612= (c.1836G>A) is low-frequency (popmax 2.24%, amr) (gnomAD).

UBTF p.Lys612=

c.1836G>A · rs140445216 · VCV3060402

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 2.24%, amr)

Conditions

UBTF-related disorder

⚠ 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 1.8	GERP -2.6, phastCons 1
Overall
CADD	12.42	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.24% Admixed American · 1,342/60,010 alleles

Filtering AF 2.14% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.1%

Overall 0.149% 2,413/1,614,152 alleles · low-frequency exomes 2,125/1,461,808 · genomes 288/152,344 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	2.24%	45
East Asian	0.936%	107
Ashkenazi Jewishnot grpmax-eligible	0.392%	255
Remaining individualsnot grpmax-eligible	0.168%	595
South Asian	0.165%	607
Finnishnot grpmax-eligible	0.0843%	1,186
African / African-American	0.0613%	1,632
Middle Eastern	0.0165%	6,062
European (non-Finnish)	0.0152%	6,592

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.Lys612=
Coding: c.1836G>A
MANE Select: NM_014233
dbSNP: rs140445216
Type: single nucleotide variant
Location: chr17:44209421 (GRCh38)

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

Disease context

UBTF-related disorder

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-lys612 (accessed [today's date]).

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