ULK4 p.Ala542=
c.1626T>C · rs374807458 · VCV787013
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.34%, afr)
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 -3.7 |
| Overall | ||
| CADD | 0.939 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.34%
African / African-American · 255/75,044 alleles
Filtering AF
0.306%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.292%
Overall
0.0181%
292/1,610,200 alleles · rare
exomes 141/1,457,842 · genomes 151/152,358 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.34% | 294 |
| Admixed American | 0.0283% | 3,530 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,670 |
| European (non-Finnish) | 0.000255% | 392,105 |
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.Ala542=
- Coding
- c.1626T>C
- MANE Select
- NM_017886
- dbSNP
- rs374807458
- Type
- single nucleotide variant
- Location
- chr3:41883904 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.59 · 2 PDB
- Residue 542
- a UniProt-annotated variant site (in)
Similar variants
- ULK4 p.Ala542Thr Benign ★★ same residue
- ULK4 c.1183-8C>A Benign ★★ same type
- ULK4 c.1288-9A>T Benign ★★ same type
- ULK4 c.1349-5C>G Benign ★★ same type
- ULK4 c.1577+10G>A Benign ★★ same type
- ULK4 c.803+3A>C Benign ★★ same type
- ULK4 p.Asn139Lys Likely benign ★★ ⚠ same type
- ULK4 p.Ile224Val Benign ★★ 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/ulk4-p-ala542 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown