UNC80 p.Thr488=
c.1464G>A · rs1241919062 · VCV1634319
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0501%, mid)
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 -1.5 | GERP -3.8 |
| Overall | ||
| CADD | 5.557 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0501%
Middle Eastern · 3/5,992 alleles
Filtering AF
0.0136%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00726%
Overall
0.00187%
29/1,551,728 alleles · ultra-rare
exomes 27/1,399,484 · genomes 2/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0501% | 1,997 |
| Remaining individualsnot grpmax-eligible | 0.00499% | 20,044 |
| Admixed American | 0.00392% | 25,502 |
| South Asian | 0.00357% | 28,019 |
| Finnishnot grpmax-eligible | 0.00334% | 29,960 |
| African / African-American | 0.00273% | 36,564 |
| East Asian | 0.00244% | 40,918 |
| European (non-Finnish) | 0.00113% | 88,232 |
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.Thr488=
- Coding
- c.1464G>A
- MANE Select
- NM_001371986
- dbSNP
- rs1241919062
- Type
- single nucleotide variant
- Location
- chr2:209817037 (GRCh38)
- Gene constraint
- LOEUF 0.48 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Similar variants
- UNC80 p.Thr488Met Uncertain significance ★★ ⚠ same residue
- 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
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-thr488 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown