ULK2 p.Lys539=
c.1617G>A · rs148364064 · VCV728214
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.16%, 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 0.18 | GERP -1.7, phastCons 0.97 |
| Overall | ||
| CADD | 7.077 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.16%
South Asian · 1,060/91,018 alleles
Filtering AF
1.11%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.08%
Overall
0.205%
3,315/1,613,752 alleles · low-frequency
exomes 2,967/1,461,752 · genomes 348/152,000 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.16% | 86 |
| Finnishnot grpmax-eligible | 0.882% | 113 |
| Ashkenazi Jewishnot grpmax-eligible | 0.75% | 133 |
| Middle Eastern | 0.413% | 242 |
| Remaining individualsnot grpmax-eligible | 0.216% | 463 |
| Admixed American | 0.15% | 666 |
| European (non-Finnish) | 0.103% | 973 |
| African / African-American | 0.00667% | 14,990 |
| East Asian | 0.00223% | 44,798 |
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
- ULK2
- Protein
- p.Lys539=
- Coding
- c.1617G>A
- MANE Select
- NM_014683
- dbSNP
- rs148364064
- Type
- single nucleotide variant
- Location
- chr17:19797588 (GRCh38)
- Gene constraint
- LOEUF 0.766 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.32 · 5 PDB
Similar variants
- ULK2 p.Arg881Gln Benign ★★ same type
- ULK2 p.Gly5= Benign ★★ same type
- ULK2 p.Tyr795= Benign ★★ same type
- ULK2 p.His578Arg Likely pathogenic ★ ⚠ same type
- ULK2 p.Ala1034Thr Uncertain significance ★ ⚠ same type
- ULK2 p.Ala264Glu Uncertain significance ★ ⚠ same type
- ULK2 p.Ala264Val Uncertain significance ★ ⚠ same type
- ULK2 p.Ala421Thr 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/ulk2-p-lys539 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown