ULK4 p.Ser883=
c.2649T>C · rs61650641 · VCV3053027
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.32%, afr)
Conditions
1
ULK4-related disorder
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 -8.5 | GERP -3.8 |
| Overall | ||
| CADD | 0.094 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.32%
African / African-American · 240/74,970 alleles
Filtering AF
0.287%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.274%
Overall
0.0171%
275/1,611,262 alleles · rare
exomes 136/1,458,972 · genomes 139/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.32% | 312 |
| Remaining individualsnot grpmax-eligible | 0.0353% | 2,837 |
| Middle Eastern | 0.0166% | 6,036 |
| Admixed American | 0.0134% | 7,470 |
| South Asian | 0.00334% | 29,975 |
| European (non-Finnish) | 8.48e-05% | 1,178,912 |
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
- ULK4
- Protein
- p.Ser883=
- Coding
- c.2649T>C
- MANE Select
- NM_017886
- dbSNP
- rs61650641
- Type
- single nucleotide variant
- Location
- chr3:41705291 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.59 · 2 PDB
Disease context
ULK4-related disorder
Similar variants
- ULK4 c.1764+3G>A Likely benign same condition
- ULK4 c.896+5T>G Likely benign same condition
- ULK4 p.Ala715Thr Benign same condition
- ULK4 p.Asn796= Likely benign same condition
- ULK4 p.Gln387Arg Likely benign same condition
- ULK4 p.Gly352= Benign same condition
- ULK4 p.His55= Likely benign same condition
- ULK4 p.Leu1084= Likely benign same condition
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/ulk4-p-ser883 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown