UNC79 p.Ser1899=
c.5697C>T · VCV4821443
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, amr)
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 -12 | GERP -4.8 |
| Overall | ||
| CADD | 0.251 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
Admixed American · 12/59,998 alleles
Filtering AF
0.0115%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00898%
Overall
0.00328%
53/1,613,958 alleles · ultra-rare
exomes 49/1,461,866 · genomes 4/152,092 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.02% | 5,000 |
| European (non-Finnish) | 0.00331% | 30,257 |
| East Asian | 0.00223% | 44,872 |
| South Asian | 0.0011% | 91,078 |
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
- UNC79
- Protein
- p.Ser1899=
- Coding
- c.5697C>T
- MANE Select
- NM_001395159
- Type
- single nucleotide variant
- Location
- chr14:93622714 (GRCh38)
- Gene constraint
- LOEUF 0.168 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.95 · 3 PDB
- Residue 1899
- the 'disordered' region
Similar variants
- UNC79 p.Ile1680Thr Uncertain significance ★★ same type
- UNC79 p.Pro2467Arg Uncertain significance ★★ same type
- UNC79 p.Ser1741Cys Uncertain significance ★★ same type
- UNC79 p.Ser706Arg Uncertain significance ★★ same type
- UNC79 p.Thr2409Met Uncertain significance ★★ same type
- UNC79 p.Tyr539Phe Uncertain significance ★★ same type
- UNC79 c.3191-2A>C Likely pathogenic ★ same type
- UNC79 c.6134-1G>A Likely pathogenic ★ 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/unc79-p-ser1899 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown