UTP4 p.Ser439=
c.1317T>A · rs200162340 · VCV2417789
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00768%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.36 | acceptor loss, 10 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP 0.38, phastCons 1 |
| Overall | ||
| CADD | 8.207 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00768%
South Asian · 7/91,088 alleles
Filtering AF
0.00359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00255%
Overall
0.00347%
56/1,614,148 alleles · very rare
exomes 52/1,461,886 · genomes 4/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00768% | 13,013 |
| African / African-American | 0.004% | 24,985 |
| European (non-Finnish) | 0.00373% | 26,820 |
| Admixed American | 0.00167% | 60,006 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,490 |
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.Ser439=
- Coding
- c.1317T>A
- MANE Select
- NM_032830
- dbSNP
- rs200162340
- Type
- single nucleotide variant
- Location
- chr16:69157113 (GRCh38)
- Gene constraint
- LOEUF 0.766 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.28 · 3 PDB
- Residue 439
- 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-ser439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown