UTP4 p.Ala178=
c.534T>C · rs766781882 · VCV3029319
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.052%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.17 | GERP -3.1 |
| Overall | ||
| CADD | 3.007 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.052%
African / African-American · 39/74,946 alleles
Filtering AF
0.039%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0346%
Overall
0.00279%
45/1,614,072 alleles · ultra-rare
exomes 22/1,461,828 · genomes 23/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.052% | 1,922 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,828 |
| Admixed American | 0.00333% | 30,006 |
| European (non-Finnish) | 8.47e-05% | 1,179,993 |
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.Ala178=
- Coding
- c.534T>C
- MANE Select
- NM_032830
- dbSNP
- rs766781882
- Type
- single nucleotide variant
- Location
- chr16:69143185 (GRCh38)
- Gene constraint
- LOEUF 0.766 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.28 · 3 PDB
- Residue 178
- a β-strand
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-ala178 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown