DONSON p.Val5=
c.15G>T · rs531692338 · VCV1633795
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0934%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.008 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -9 |
| Overall | ||
| CADD | 0.521 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0934%
African / African-American · 60/64,268 alleles
Filtering AF
0.0744%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0676%
Overall
0.00556%
69/1,241,862 alleles · ultra-rare
exomes 27/1,089,888 · genomes 42/151,974 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0934% | 1,071 |
| Middle Eastern | 0.031% | 3,222 |
| East Asian | 0.00956% | 10,455 |
| Remaining individualsnot grpmax-eligible | 0.00437% | 22,904 |
| Admixed American | 0.00418% | 23,950 |
| South Asian | 0.00334% | 29,962 |
| Finnishnot grpmax-eligible | 0.0031% | 32,256 |
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
- DONSON
- Protein
- p.Val5=
- Coding
- c.15G>T
- MANE Select
- NM_017613
- dbSNP
- rs531692338
- Type
- single nucleotide variant
- Location
- chr21:33588627 (GRCh38)
- Gene constraint
- LOEUF 0.918 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.94
- Residue 5
- the 'disordered' region
Similar variants
- DONSON c.1047-9A>G Pathogenic ★★ same type
- DONSON c.1563+1G>T Pathogenic ★★ same type
- DONSON p.Arg293Ter Pathogenic ★★ same type
- DONSON p.Arg442Ter Pathogenic ★★ same type
- DONSON p.Gln428Ter Pathogenic/Likely pathogenic ★★ same type
- DONSON p.Phe165Ser Pathogenic/Likely pathogenic ★★ same type
- DONSON p.Ala32Gly Uncertain significance ★★ ⚠ same type
- DONSON p.Ala429Glu 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/donson-p-val5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown