UTP4 p.Pro155=
c.465C>T · rs535751187 · VCV2712960
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0118%, nfe)
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 -2.9 | GERP -5.9 |
| Overall | ||
| CADD | 7.871 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0118%
European (non-Finnish) · 139/1,179,854 alleles
Filtering AF
0.0102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00956%
Overall
0.00898%
145/1,613,910 alleles · ultra-rare
exomes 140/1,461,680 · genomes 5/152,230 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0118% | 8,488 |
| African / African-American | 0.00533% | 18,755 |
| Admixed American | 0.00167% | 60,006 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,502 |
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.Pro155=
- Coding
- c.465C>T
- MANE Select
- NM_032830
- dbSNP
- rs535751187
- Type
- single nucleotide variant
- Location
- chr16:69139853 (GRCh38)
- Gene constraint
- LOEUF 0.766 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.28 · 3 PDB
Similar variants
- UTP4 p.Pro155His Likely benign ★ same residue
- 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
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-pro155 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown