UNC80 p.Ala3099=
c.9297C>T · rs879405779 · VCV1553481
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00628%, nfe)
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 |
|---|---|---|
| Pangolin | Δ0.20 | loss · gain 0.00 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP -5.1 | GERP -5.4 |
| Overall | ||
| CADD | 2.932 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00628%
European (non-Finnish) · 72/1,146,678 alleles
Filtering AF
0.00509%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00468%
Overall
0.00497%
77/1,550,836 alleles · very rare
exomes 75/1,398,824 · genomes 2/152,012 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00628% | 15,926 |
| African / African-American | 0.00411% | 24,310 |
| East Asian | 0.00245% | 40,896 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 60,052 |
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
- UNC80
- Protein
- p.Ala3099=
- Coding
- c.9297C>T
- MANE Select
- NM_001371986
- dbSNP
- rs879405779
- Type
- single nucleotide variant
- Location
- chr2:209984895 (GRCh38)
- Gene constraint
- LOEUF 0.48 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 3099
- the 'disordered' region
Similar variants
- UNC80 c.4110+1G>C Pathogenic/Likely pathogenic ★★ same type
- UNC80 c.7287-1G>A Likely pathogenic ★★ same type
- UNC80 c.8772+1G>A Likely pathogenic ★★ same type
- UNC80 p.Arg1069Ter Pathogenic ★★ same type
- UNC80 p.Arg1076Ter Pathogenic ★★ same type
- UNC80 p.Arg1110Ter Pathogenic ★★ same type
- UNC80 p.Arg1179Ter Pathogenic/Likely pathogenic ★★ same type
- UNC80 p.Arg1285Ter 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/unc80-p-ala3099 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown