ULK1 p.Ala923=
c.2769C>T · rs143340589 · VCV718865
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.721%, 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 -20 | GERP -3.2 |
| Overall | ||
| CADD | 0.246 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.721%
African / African-American · 541/75,046 alleles
Filtering AF
0.671%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.651%
Overall
0.0506%
815/1,612,200 alleles · rare
exomes 429/1,459,850 · genomes 386/152,350 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.721% | 139 |
| Admixed American | 0.0883% | 1,132 |
| Remaining individualsnot grpmax-eligible | 0.0641% | 1,561 |
| Finnishnot grpmax-eligible | 0.0496% | 2,017 |
| Middle Eastern | 0.0165% | 6,058 |
| European (non-Finnish) | 0.012% | 8,307 |
| South Asian | 0.00659% | 15,182 |
| East Asian | 0.00223% | 44,882 |
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.Ala923=
- Coding
- c.2769C>T
- MANE Select
- NM_003565
- dbSNP
- rs143340589
- Type
- single nucleotide variant
- Location
- chr12:131919556 (GRCh38)
- Gene constraint
- LOEUF 0.61 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.99 · 19 PDB
- Residue 923
- the 'c-terminal domain; mediates interaction with sesn2' region
Similar variants
- ULK1 p.Thr660Met Uncertain significance ★★ ⚠ 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
- ULK1 p.Pro574Arg 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-ala923 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown