UBASH3A p.Phe304=
c.912T>C · rs61735849 · VCV769477
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.98%, afr) — too common for a highly-penetrant pathogenic allele
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 -6.1 | GERP -4 |
| Overall | ||
| CADD | 4.154 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.98%
African / African-American · 4,487/75,050 alleles
Filtering AF
5.83%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.77%
Overall
0.327%
5,279/1,614,224 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.98% | 17 |
| Admixed American | 0.521% | 192 |
| Remaining individualsnot grpmax-eligible | 0.507% | 197 |
| Middle Eastern | 0.379% | 264 |
| South Asian | 0.011% | 9,109 |
| European (non-Finnish) | 0.0108% | 9,219 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
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
- UBASH3A
- Protein
- p.Phe304=
- Coding
- c.912T>C
- MANE Select
- NM_018961
- dbSNP
- rs61735849
- Type
- single nucleotide variant
- Location
- chr21:42418475 (GRCh38)
- Gene constraint
- LOEUF 1.038 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.62 · 2 PDB
- Residue 304
- the sh3 domain
Similar variants
- UBASH3A p.Ile463Phe Uncertain significance ★★ ⚠ same type
- CLIP4 p.Thr555= Benign ★★ same type
- UBASH3A c.1393+3A>C Benign ★★ same type
- UBASH3A p.Gly601= Benign ★★ same type
- UBASH3A p.Ile303= Benign ★★ same type
- UBASH3A p.Ile658Val Benign ★★ same type
- UBASH3A p.Thr144= Benign ★★ same type
- UBASH3A p.Thr392= 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/ubash3a-p-phe304 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown