Is UTP4 p.Asp289= (c.867C>T) pathogenic?

UTP4 p.Asp289= (c.867C>T) is classified Likely benign in UTP4 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-02). Ultra-rare (popmax 0.0133%, amr).

How common is UTP4 p.Asp289= (c.867C>T) in the general population?

UTP4 p.Asp289= (c.867C>T) is ultra-rare (popmax 0.0133%, amr) (gnomAD).

UTP4 p.Asp289=

c.867C>T · rs771955667 · VCV2895601

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.82 · evaluated, not missing
Constraint at this position
Conservation	phyloP -13	GERP -5.1
Overall
CADD	1.703	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0133% Admixed American · 8/60,004 alleles

Filtering AF 0.00661% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00482%

Overall 0.00161% 26/1,614,092 alleles · ultra-rare exomes 23/1,461,888 · genomes 3/152,204 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0133%	7,501
Remaining individualsnot grpmax-eligible	0.0064%	15,622
South Asian	0.00329%	30,363
East Asian	0.00223%	44,888
European (non-Finnish)	0.000847%	118,005

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.Asp289=
Coding: c.867C>T
MANE Select: NM_032830
dbSNP: rs771955667
Type: single nucleotide variant
Location: chr16:69150665 (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

Similar variants

UTP4 c.1287+6T>C Uncertain significance ★★ same type
UTP4 c.1444+6A>C Uncertain significance ★★ same type
UTP4 p.Arg291His Uncertain significance ★★ ⚠ same type
UTP4 p.Arg417Trp Uncertain significance ★★ ⚠ same type
UTP4 p.Arg634Gln Uncertain significance ★★ ⚠ same type
UTP4 p.Asn25Ser Uncertain significance ★★ ⚠ same type
UTP4 p.Asn537Ser Uncertain significance ★★ ⚠ same type
UTP4 p.Gly459Glu 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/utp4-p-asp289 (accessed [today's date]).

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