CUX1 p.Ser1098=
c.3294C>T · rs151241171 · VCV2657871
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.104%, 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 -4.8 | GERP -5.6 |
| Overall | ||
| CADD | 0.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.104%
European (non-Finnish) · 1,227/1,180,036 alleles
Filtering AF
0.0991%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0971%
Overall
0.0851%
1,374/1,614,122 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.104% | 962 |
| Remaining individualsnot grpmax-eligible | 0.0816% | 1,226 |
| South Asian | 0.056% | 1,786 |
| Finnishnot grpmax-eligible | 0.0375% | 2,667 |
| Admixed American | 0.02% | 5,001 |
| African / African-American | 0.012% | 8,336 |
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
- CUX1
- Protein
- p.Ser1098=
- Coding
- c.3294C>T
- MANE Select
- NM_181552
- dbSNP
- rs151241171
- Type
- single nucleotide variant
- Location
- chr7:102227530 (GRCh38)
- Gene constraint
- LOEUF 0.277 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.84 · 3 PDB
- Residue 1098
- the 'disordered' region; a UniProt-annotated variant site (in neddms)
Similar variants
- CUX1 c.1451-2A>G Likely pathogenic ★★ same type
- CUX1 c.1681-1G>A Pathogenic/Likely pathogenic ★★ same type
- CUX1 p.Arg661Ter Pathogenic/Likely pathogenic ★★ same type
- CUX1 p.Gln862Ter Pathogenic/Likely pathogenic ★★ same type
- CUX1 p.Glu866Ter Pathogenic/Likely pathogenic ★★ same type
- CUX1 p.Trp1188Ter Pathogenic ★★ same type
- CUX1 p.Ala1433Val Uncertain significance ★★ ⚠ same type
- CUX1 p.Ala454Val 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/cux1-p-ser1098 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown