ULK4 p.Ser292=
c.876C>T · rs371153917 · VCV3041376
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.239%, 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 1.1 | GERP -1.4 |
| Overall | ||
| CADD | 5.732 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.239%
African / African-American · 179/75,014 alleles
Filtering AF
0.21%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.199%
Overall
0.0167%
269/1,614,058 alleles · rare
exomes 144/1,461,796 · genomes 125/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.239% | 419 |
| Middle Eastern | 0.0495% | 2,020 |
| Admixed American | 0.04% | 2,501 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,464 |
| European (non-Finnish) | 0.0039% | 25,652 |
| East Asian | 0.00223% | 44,858 |
| South Asian | 0.0022% | 45,541 |
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.Ser292=
- Coding
- c.876C>T
- MANE Select
- NM_017886
- dbSNP
- rs371153917
- Type
- single nucleotide variant
- Location
- chr3:41912827 (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-ser292 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown