UPF1 p.Ser417=
c.1251G>A · rs114623873 · VCV788468
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.03%, 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 -4.3 | GERP -2.8 |
| Overall | ||
| CADD | 1.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.03%
African / African-American · 774/75,044 alleles
Filtering AF
0.971%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.947%
Overall
0.0564%
910/1,613,792 alleles · low-frequency
exomes 435/1,461,476 · genomes 475/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.03% | 97 |
| Admixed American | 0.1% | 1,000 |
| Remaining individualsnot grpmax-eligible | 0.0704% | 1,420 |
| Middle Eastern | 0.034% | 2,940 |
| East Asian | 0.00891% | 11,220 |
| South Asian | 0.00769% | 13,010 |
| European (non-Finnish) | 0.00161% | 62,103 |
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
- UPF1
- Protein
- p.Ser417=
- Coding
- c.1251G>A
- MANE Select
- NM_002911
- dbSNP
- rs114623873
- Type
- single nucleotide variant
- Location
- chr19:18854695 (GRCh38)
- Gene constraint
- LOEUF 0.125 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.58 · 12 PDB
Similar variants
- UPF1 c.1266-32T>G Benign ★★ same type
- UPF1 c.1544+108G>A Benign ★★ same type
- UPF1 c.2300+75T>C Benign ★★ same type
- UPF1 c.232-90G>A Benign ★★ same type
- UPF1 c.2457+89G>A Benign ★★ same type
- UPF1 c.2458-85G>T Benign ★★ same type
- UPF1 c.2601-188G>C Benign ★★ same type
- UPF1 c.2601-47A>G Benign ★★ 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/upf1-p-ser417 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown