UNC80 p.Arg1874=
c.5622C>T · rs759269541 · VCV1476603
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0204%, nfe)
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 -0.99 | GERP -3.7 |
| Overall | ||
| CADD | 2.725 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0204%
European (non-Finnish) · 234/1,146,992 alleles
Filtering AF
0.0182%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0174%
Overall
0.0159%
247/1,551,718 alleles · ultra-rare
exomes 230/1,399,584 · genomes 17/152,134 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0204% | 4,902 |
| Remaining individualsnot grpmax-eligible | 0.0116% | 8,597 |
| African / African-American | 0.00274% | 36,507 |
| East Asian | 0.00244% | 40,928 |
| South Asian | 0.00238% | 42,029 |
| Admixed American | 0.00196% | 50,972 |
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.Arg1874=
- Coding
- c.5622C>T
- MANE Select
- NM_001371986
- dbSNP
- rs759269541
- Type
- single nucleotide variant
- Location
- chr2:209922343 (GRCh38)
- Gene constraint
- LOEUF 0.48 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 1874
- an α-helix
Similar variants
- UNC80 p.Arg1874Cys 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-arg1874 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown