ULK2 p.Ser780=
c.2340C>T · rs56181782 · VCV2647564
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.632%, nfe)
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 -0.017 | GERP -0.51, phastCons 0.29 |
| Overall | ||
| CADD | 7.786 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.632%
European (non-Finnish) · 7,423/1,174,376 alleles
Filtering AF
0.62%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.615%
Overall
0.503%
8,058/1,602,896 alleles · rare
exomes 7,488/1,450,534 · genomes 570/152,362 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.632% | 158 |
| Remaining individualsnot grpmax-eligible | 0.364% | 275 |
| Finnishnot grpmax-eligible | 0.338% | 296 |
| Admixed American | 0.104% | 961 |
| African / African-American | 0.083% | 1,204 |
| Middle Eastern | 0.0671% | 1,490 |
| South Asian | 0.0656% | 1,525 |
| Ashkenazi Jewishnot grpmax-eligible | 0.017% | 5,897 |
| East Asian | 0.00677% | 14,775 |
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.Ser780=
- Coding
- c.2340C>T
- MANE Select
- NM_014683
- dbSNP
- rs56181782
- Type
- single nucleotide variant
- Location
- chr17:19783817 (GRCh38)
- Gene constraint
- LOEUF 0.766 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.32 · 5 PDB
- Residue 780
- a modified residue (phosphoserine)
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-ser780 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown