UNC119 p.Ile86=
c.258C>T · rs767872520 · VCV3040919
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0198%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.26 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.6 | GERP -3.9 |
| Overall | ||
| CADD | 12.84 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0198%
South Asian · 18/91,088 alleles
Filtering AF
0.0127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0105%
Overall
0.00173%
28/1,614,036 alleles · ultra-rare
exomes 26/1,461,830 · genomes 2/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0198% | 5,060 |
| East Asian | 0.00223% | 44,884 |
| Admixed American | 0.00167% | 60,008 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| European (non-Finnish) | 0.000593% | 168,575 |
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
- UNC119
- Protein
- p.Ile86=
- Coding
- c.258C>T
- MANE Select
- NM_005148
- dbSNP
- rs767872520
- Type
- single nucleotide variant
- Location
- chr17:28548668 (GRCh38)
- Gene constraint
- LOEUF 1.139 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.03 · 9 PDB
- Residue 86
- a UniProt-annotated variant site (in cord24; when expressed in transgenic mice, it results in age-dependent fundus lesions, defects in photoreceptor synaptic transmission and retinal degeneration)
Similar variants
- UNC119 p.Arg113Trp Uncertain significance ★★ ⚠ same type
- UNC119 p.Arg118Gln Uncertain significance ★★ ⚠ same type
- UNC119 p.Arg118Trp Uncertain significance ★★ ⚠ same type
- UNC119 p.Arg119Trp Uncertain significance ★★ ⚠ same type
- UNC119 p.Arg127Cys Uncertain significance ★★ ⚠ same type
- UNC119 p.Arg127His Uncertain significance ★★ ⚠ same type
- UNC119 p.Arg130Cys Uncertain significance ★★ ⚠ same type
- UNC119 p.Arg139Ser Uncertain significance ★★ ⚠ 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/unc119-p-ile86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown