ULK3 p.Ser468=
c.1404T>G · rs55973697 · VCV787681
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.66%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -4.3 |
| Overall | ||
| CADD | 0.437 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.66%
European (non-Finnish) · 19,357/1,163,058 alleles
Filtering AF
1.64%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.64%
Overall
1.3%
20,653/1,583,116 alleles · low-frequency
exomes 19,354/1,431,032 · genomes 1,299/152,084 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.66% | 60 |
| Remaining individualsnot grpmax-eligible | 1.19% | 84 |
| Admixed American | 0.4% | 250 |
| African / African-American | 0.224% | 446 |
| Finnishnot grpmax-eligible | 0.186% | 539 |
| Ashkenazi Jewishnot grpmax-eligible | 0.159% | 630 |
| Middle Eastern | 0.0338% | 2,956 |
| South Asian | 0.00938% | 10,665 |
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
- ULK3
- Protein
- p.Ser468=
- Coding
- c.1404T>G
- MANE Select
- NM_001099436
- dbSNP
- rs55973697
- Type
- single nucleotide variant
- Location
- chr15:74837243 (GRCh38)
- Gene constraint
- LOEUF 1.161 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.96 · 3 PDB
Similar variants
- ULK3 p.Arg101His Benign ★★ same type
- ULK3 p.Pro177= Benign ★★ same type
- ULK3 p.Ala114Val Uncertain significance ★ ⚠ same type
- ULK3 p.Ala192Thr Uncertain significance ★ ⚠ same type
- ULK3 p.Ala26Thr Uncertain significance ★ ⚠ same type
- ULK3 p.Ala286Val Uncertain significance ★ ⚠ same type
- ULK3 p.Ala303Thr Uncertain significance ★ ⚠ same type
- ULK3 p.Ala378Thr 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/ulk3-p-ser468 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown