ULK1 p.Ala393=
c.1179G>T · rs142630747 · VCV2643611
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0302%, 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 -2.9 | GERP -2.4 |
| Overall | ||
| CADD | 1.208 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0302%
South Asian · 26/86,130 alleles
Filtering AF
0.0211%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0181%
Overall
0.00172%
27/1,566,126 alleles · ultra-rare
exomes 25/1,414,484 · genomes 2/151,642 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0302% | 3,313 |
| European (non-Finnish) | 8.65e-05% | 1,156,238 |
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
- ULK1
- Protein
- p.Ala393=
- Coding
- c.1179G>T
- MANE Select
- NM_003565
- dbSNP
- rs142630747
- Type
- single nucleotide variant
- Location
- chr12:131913768 (GRCh38)
- Gene constraint
- LOEUF 0.61 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.99 · 19 PDB
- Residue 393
- the 'interaction with gabarap and gabarapl2' region; the 'disordered' region
Similar variants
- ULK1 p.Ala393Val Uncertain significance ★ ⚠ same residue
- ULK1 p.Thr660Met Uncertain significance ★★ ⚠ same type
- ULK1 p.Ala923= Benign ★★ same type
- ULK1 p.Arg966= Benign ★★ same type
- ULK1 p.Gly757= Benign ★★ same type
- ULK1 p.Leu596= Benign ★★ same type
- ULK1 p.Leu926= Benign ★★ same type
- ULK1 p.Leu957= Benign/Likely benign ★★ 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/ulk1-p-ala393 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown