Is UTP4 p.Ser467= (c.1401A>T) pathogenic?

UTP4 p.Ser467= (c.1401A>T) is classified Likely benign in UTP4 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-10-12). Very rare (popmax 8.47e-05%, nfe); Associated with UTP4-related disorder.

What condition is associated with UTP4 p.Ser467= (c.1401A>T)?

UTP4 p.Ser467= (c.1401A>T) is associated with UTP4-related disorder (ClinVar).

How common is UTP4 p.Ser467= (c.1401A>T) in the general population?

UTP4 p.Ser467= (c.1401A>T) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

UTP4 p.Ser467=

c.1401A>T · rs1963440330 · VCV3044288

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

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 -0.044	GERP -2.2
Overall
CADD	1.558	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,046 alleles

Overall 6.19e-05% 1/1,614,210 alleles · very rare exomes 1/1,461,868 · genomes 0/152,342 · joint denominator

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: UTP4
Protein: p.Ser467=
Coding: c.1401A>T
MANE Select: NM_032830
dbSNP: rs1963440330
Type: single nucleotide variant
Location: chr16:69157197 (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-ser467 (accessed [today's date]).

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