Is UBA6 p.Ser360Phe (c.1079C>T) pathogenic?

UBA6 p.Ser360Phe (c.1079C>T) is classified Uncertain significance in UBA6 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-03). AlphaMissense: likely benign (0.1203); Absent from gnomAD v4.1.

How common is UBA6 p.Ser360Phe (c.1079C>T) in the general population?

UBA6 p.Ser360Phe (c.1079C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about UBA6 p.Ser360Phe (c.1079C>T)?

AlphaMissense predicts likely benign (score 0.1203) — an in-silico prediction, not a clinical call.

UBA6 p.Ser360Phe

c.1079C>T · VCV3464940

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1203 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1203	likely benign
REVEL	0.141	moderately benign-leaning
SaProt	LLR -10.13	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2.4	GERP -1.2, phastCons 0.99
Regional constraint	o/e 0.96	unconstrained · MANE · 82 kb · p 0.12 · regional, not allelic
Overall
CADD	21.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: UBA6
Protein: p.Ser360Phe
Coding: c.1079C>T
MANE Select: NM_018227
Type: single nucleotide variant
Location: chr4:67662214 (GRCh38)
Gene constraint: LOEUF 0.868 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.67 · 20 PDB
Residue 360: an α-helix

Full UBA6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

UBA6 p.Ala526Val Uncertain significance ★ ⚠ same type
UBA6 p.Ala540Val Uncertain significance ★ ⚠ same type
UBA6 p.Ala55Gly Uncertain significance ★ same type
UBA6 p.Ala567Val Uncertain significance ★ ⚠ same type
UBA6 p.Ala824Val Uncertain significance ★ ⚠ same type
UBA6 p.Arg248Gln Uncertain significance ★ ⚠ same type
UBA6 p.Arg513Cys Uncertain significance ★ same type
UBA6 p.Arg513His Uncertain significance ★ ⚠ same type

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/uba6-p-ser360phe (accessed [today's date]).

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