UNC79 p.Ala2389=
c.7167G>A · VCV4533855
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.111%, eas)
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 -1.2 | GERP -4.7 |
| Overall | ||
| CADD | 6.914 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.111%
East Asian · 50/44,880 alleles
Filtering AF
0.0867%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0781%
Overall
0.00892%
144/1,614,164 alleles · rare
exomes 113/1,461,840 · genomes 31/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.111% | 898 |
| Remaining individualsnot grpmax-eligible | 0.056% | 1,786 |
| South Asian | 0.0318% | 3,141 |
| African / African-American | 0.0293% | 3,411 |
| Admixed American | 0.00833% | 12,006 |
| European (non-Finnish) | 0.000254% | 393,334 |
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
- UNC79
- Protein
- p.Ala2389=
- Coding
- c.7167G>A
- MANE Select
- NM_001395159
- Type
- single nucleotide variant
- Location
- chr14:93686586 (GRCh38)
- Gene constraint
- LOEUF 0.168 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.95 · 3 PDB
- Residue 2389
- an α-helix
Similar variants
- UNC79 p.Ile1680Thr Uncertain significance ★★ same type
- UNC79 p.Pro2467Arg Uncertain significance ★★ same type
- UNC79 p.Ser1741Cys Uncertain significance ★★ same type
- UNC79 p.Ser706Arg Uncertain significance ★★ same type
- UNC79 p.Thr2409Met Uncertain significance ★★ same type
- UNC79 p.Tyr539Phe Uncertain significance ★★ same type
- UNC79 c.3191-2A>C Likely pathogenic ★ same type
- UNC79 c.6134-1G>A 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/unc79-p-ala2389 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown