UNC80 p.Phe1033=
c.3099C>T · rs768500267 · VCV2964079
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.025%, sas)
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 2.8 | GERP 0.5, phastCons 1 |
| Overall | ||
| CADD | 12.64 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.025%
South Asian · 21/84,052 alleles
Filtering AF
0.0167%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.014%
Overall
0.00142%
22/1,551,578 alleles · ultra-rare
exomes 20/1,399,414 · genomes 2/152,164 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.025% | 4,002 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,118 |
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.Phe1033=
- Coding
- c.3099C>T
- MANE Select
- NM_001371986
- dbSNP
- rs768500267
- Type
- single nucleotide variant
- Location
- chr2:209839279 (GRCh38)
- Gene constraint
- LOEUF 0.48 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
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-phe1033 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown