ULK1 p.Ile1027=
c.3081C>T · VCV4822036
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00934%, afr)
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 -0.76 | GERP -3.4, phastCons 0.002 |
| Overall | ||
| CADD | 2.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00934%
African / African-American · 7/74,930 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.00367%
59/1,607,228 alleles · very rare
exomes 50/1,455,022 · genomes 9/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00934% | 10,704 |
| European (non-Finnish) | 0.00407% | 24,579 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,598 |
| East Asian | 0.00223% | 44,876 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,420 |
| South Asian | 0.0011% | 91,088 |
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.Ile1027=
- Coding
- c.3081C>T
- MANE Select
- NM_003565
- Type
- single nucleotide variant
- Location
- chr12:131921219 (GRCh38)
- Gene constraint
- LOEUF 0.61 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.99 · 19 PDB
- Residue 1027
- the 'c-terminal domain; mediates interaction with sesn2' region
Similar variants
- 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
- ULK1 p.Pro574= 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-ile1027 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown