UTP4 p.Ala501=
c.1503A>C · rs1203360706 · VCV3060618
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
1
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 -1.2 | GERP -5.8 |
| Overall | ||
| CADD | 2.622 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,920 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000186%
3/1,614,056 alleles · very rare
exomes 1/1,461,880 · genomes 2/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 74,920 |
| European (non-Finnish) | 0.000169% | 590,012 |
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.Ala501=
- Coding
- c.1503A>C
- MANE Select
- NM_032830
- dbSNP
- rs1203360706
- Type
- single nucleotide variant
- Location
- chr16:69160414 (GRCh38)
- Gene constraint
- LOEUF 0.766 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.28 · 3 PDB
- Residue 501
- a β-strand
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-ala501 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown