ULK2 p.Gln676=
c.2028A>G · rs1443611505 · VCV2647565
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
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 -0.095 | GERP -1.6, phastCons 0.86 |
| Overall | ||
| CADD | 4.815 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,008 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000805%
13/1,614,016 alleles · very rare
exomes 12/1,461,798 · genomes 1/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 20,003 |
| European (non-Finnish) | 0.000847% | 118,001 |
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.Gln676=
- Coding
- c.2028A>G
- MANE Select
- NM_014683
- dbSNP
- rs1443611505
- Type
- single nucleotide variant
- Location
- chr17:19795695 (GRCh38)
- Gene constraint
- LOEUF 0.766 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.32 · 5 PDB
- Residue 676
- the 'disordered' region
Similar variants
- ULK2 p.Arg881Gln Benign ★★ same type
- ULK2 p.Gly5= Benign ★★ same type
- ULK2 p.Lys539= 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
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-gln676 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown