U2AF2 p.Ser438=
c.1314T>A · VCV4944031
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.636%, 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 -2.8 | GERP -1.6 |
| Overall | ||
| CADD | 6.405 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.636%
African / African-American · 477/75,034 alleles
Filtering AF
0.589%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.57%
Overall
0.0345%
556/1,613,644 alleles · rare
exomes 282/1,461,336 · genomes 274/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.636% | 157 |
| Admixed American | 0.0467% | 2,141 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,155 |
| Middle Eastern | 0.0165% | 6,058 |
| South Asian | 0.0033% | 30,338 |
| European (non-Finnish) | 0.00153% | 65,542 |
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
- U2AF2
- Protein
- p.Ser438=
- Coding
- c.1314T>A
- MANE Select
- NM_007279
- Type
- single nucleotide variant
- Location
- chr19:55673954 (GRCh38)
- Gene constraint
- LOEUF 0.209 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.24 · 40 PDB
- Residue 438
- the rrm 3 domain; a β-strand
Similar variants
- U2AF2 p.Arg149Gln Pathogenic/Likely pathogenic ★★ same type
- U2AF2 p.Arg149Trp Pathogenic ★★ same type
- U2AF2 p.Arg150Cys Pathogenic/Likely pathogenic ★★ same type
- U2AF2 p.Arg150His Pathogenic/Likely pathogenic ★★ same type
- U2AF2 p.Val153Met Pathogenic ★★ same type
- U2AF2 p.His470Gln Uncertain significance ★★ ⚠ same type
- U2AF2 p.Asp391= Likely benign ★★ same type
- U2AF2 p.Ser243= Likely 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/u2af2-p-ser438 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown