CUTA p.Arg86=
c.258G>A · rs374469503 · VCV2511428
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00237%, 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 2.2 | GERP -0.33, phastCons 1 |
| Overall | ||
| CADD | 15.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00237%
European (non-Finnish) · 28/1,180,042 alleles
Filtering AF
0.00164%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00142%
Overall
0.0018%
29/1,614,050 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00237% | 42,144 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
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
- CUTA
- Protein
- p.Arg86=
- Coding
- c.258G>A
- MANE Select
- NM_001014840
- dbSNP
- rs374469503
- Type
- single nucleotide variant
- Location
- chr6:33417310 (GRCh38)
- Gene constraint
- LOEUF 1.358 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.16 · 2 PDB
- Residue 86
- an α-helix
Similar variants
- CUTA c.44C>A Uncertain significance ★ same type
- CUTA p.Ala12Val Uncertain significance ★ same type
- CUTA p.Ala94Thr Uncertain significance ★ ⚠ same type
- CUTA p.Arg138Cys Uncertain significance ★ ⚠ same type
- CUTA p.Arg165Cys Uncertain significance ★ ⚠ same type
- CUTA p.Asn98Ile Uncertain significance ★ ⚠ same type
- CUTA p.Glu144Lys Uncertain significance ★ ⚠ same type
- CUTA p.Gly10Glu 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/cuta-p-arg86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown