ULK4 p.Arg739=
c.2217T>C · rs192020899 · VCV2653697
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.138%, 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 -0.42 | GERP -3.5 |
| Overall | ||
| CADD | 0.413 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.138%
European (non-Finnish) · 1,629/1,179,752 alleles
Filtering AF
0.132%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.13%
Overall
0.109%
1,765/1,613,520 alleles · rare
exomes 1,619/1,461,288 · genomes 146/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.138% | 724 |
| Remaining individualsnot grpmax-eligible | 0.088% | 1,136 |
| Admixed American | 0.0734% | 1,362 |
| Middle Eastern | 0.0497% | 2,014 |
| Finnishnot grpmax-eligible | 0.0188% | 5,333 |
| African / African-American | 0.0133% | 7,501 |
| South Asian | 0.0132% | 7,579 |
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.Arg739=
- Coding
- c.2217T>C
- MANE Select
- NM_017886
- dbSNP
- rs192020899
- Type
- single nucleotide variant
- Location
- chr3:41754465 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.59 · 2 PDB
Similar variants
- ULK4 p.Arg739His Uncertain significance ★ ⚠ 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.Ala542Thr Benign ★★ same type
- ULK4 p.Asn139Lys Likely 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-arg739 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown