UPF3B p.Arg348=
c.1044G>A · rs755604915 · VCV2661307
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0118%, eas)
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 -0.18 | GERP -3.5, phastCons 0.39 |
| Overall | ||
| CADD | 3.997 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0118%
East Asian · 4/33,853 alleles
Filtering AF
0.00395%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00235%
Overall
0.00033%
4/1,210,988 alleles · ultra-rare
exomes 4/1,097,783 · genomes 0/113,205 · joint denominator
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
- UPF3B
- Protein
- p.Arg348=
- Coding
- c.1044G>A
- MANE Select
- NM_080632
- dbSNP
- rs755604915
- Type
- single nucleotide variant
- Location
- chrX:119838015 (GRCh38)
- Structure
- AlphaFold pLDDT 67.35 · 3 PDB
- Residue 348
- the 'disordered' region
Similar variants
- UPF3B p.Arg348Gly Uncertain significance ★ ⚠ same residue
- UPF3B p.Arg13Ter Likely pathogenic ★★ same type
- UPF3B p.Arg354Ter Likely pathogenic ★★ same type
- UPF3B p.Arg229Lys Uncertain significance ★★ ⚠ same type
- UPF3B p.Arg255Gly Uncertain significance ★★ same type
- UPF3B p.Arg259Lys Uncertain significance ★★ ⚠ same type
- UPF3B p.Arg313Gly Uncertain significance ★★ ⚠ same type
- UPF3B p.Arg350Gln 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/upf3b-p-arg348 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown