Is UBTF p.Phe361= (c.1083C>T) pathogenic?

UBTF p.Phe361= (c.1083C>T) is classified Likely benign in UBTF (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-31). Very rare (popmax 0.00668%, eas).

How common is UBTF p.Phe361= (c.1083C>T) in the general population?

UBTF p.Phe361= (c.1083C>T) is very rare (popmax 0.00668%, eas) (gnomAD).

UBTF p.Phe361=

c.1083C>T · VCV4935395

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00668%, eas)

⚠ 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 0.11	GERP -4.2, phastCons 0.38
Overall
CADD	6.832	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00668% East Asian · 3/44,884 alleles

Filtering AF 0.00177% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000891%

Overall 0.000681% 11/1,614,242 alleles · very rare exomes 11/1,461,882 · genomes 0/152,360 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00668%	14,961
Remaining individualsnot grpmax-eligible	0.0016%	62,508
European (non-Finnish)	0.000593%	168,579

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.Phe361=
Coding: c.1083C>T
MANE Select: NM_014233
Type: single nucleotide variant
Location: chr17:44211296 (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-phe361 (accessed [today's date]).

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