Is UTP4 p.Ile583= (c.1749C>T) pathogenic?

UTP4 p.Ile583= (c.1749C>T) is classified Likely benign in UTP4 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-08-27). Absent from gnomAD v4.1; Associated with UTP4-related disorder.

What condition is associated with UTP4 p.Ile583= (c.1749C>T)?

UTP4 p.Ile583= (c.1749C>T) is associated with UTP4-related disorder (ClinVar).

How common is UTP4 p.Ile583= (c.1749C>T) in the general population?

UTP4 p.Ile583= (c.1749C>T) is absent from gnomAD v4.1 (gnomAD).

UTP4 p.Ile583=

c.1749C>T · VCV3344359

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

UTP4-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2	GERP -1.3, phastCons 1
Overall
CADD	9.031	PHRED · no single calibrated threshold — expert panels disagree

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: UTP4
Protein: p.Ile583=
Coding: c.1749C>T
MANE Select: NM_032830
Type: single nucleotide variant
Location: chr16:69165442 (GRCh38)
Gene constraint: LOEUF 0.766 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.28 · 3 PDB

Full UTP4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

UTP4-related disorder

Similar variants

UTP4 p.Asn537Ser Uncertain significance ★★ ⚠ same condition
UTP4 p.Val522Met Uncertain significance ★★ ⚠ same condition
UTP4 p.Asn80His Uncertain significance ★ ⚠ same condition
UTP4 p.Phe311Leu Uncertain significance ★ ⚠ same condition
UTP4 p.Cys340Gly Uncertain significance same condition
UTP4 p.Cys520Tyr Uncertain significance ⚠ same condition
UTP4 p.Ile160Val Uncertain significance ⚠ same condition
UTP4 p.Pro649His Uncertain significance ⚠ same condition

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/utp4-p-ile583 (accessed [today's date]).

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