CYC1 p.Asp86=
c.258C>T · rs200527190 · VCV2140458
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.26 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.33 | GERP -2.1, phastCons 0.95 |
| Overall | ||
| CADD | 7.873 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,072 alleles
Filtering AF
0.00791%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00744%
Overall
0.0079%
127/1,608,084 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,072 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,242 |
| European (non-Finnish) | 0.00941% | 10,628 |
| Admixed American | 0.00501% | 19,970 |
| African / African-American | 0.00134% | 74,854 |
| South Asian | 0.0011% | 91,054 |
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
- CYC1
- Protein
- p.Asp86=
- Coding
- c.258C>T
- MANE Select
- NM_001916
- dbSNP
- rs200527190
- Type
- single nucleotide variant
- Location
- chr8:144095961 (GRCh38)
- Gene constraint
- LOEUF 0.583 · pLI 0.85 (gnomAD)
- Structure
- AlphaFold pLDDT 86.37 · 5 PDB
Similar variants
- CYC1 p.Ala4Val Uncertain significance ★★ ⚠ same type
- CYC1 p.Ala5Thr Uncertain significance ★★ ⚠ same type
- CYC1 p.Arg285Gln Uncertain significance ★★ ⚠ same type
- CYC1 p.Arg287His Uncertain significance ★★ ⚠ same type
- CYC1 p.Arg308Gln Uncertain significance ★★ ⚠ same type
- CYC1 p.Asn159Ser Uncertain significance ★★ ⚠ same type
- CYC1 p.Asp173Asn Uncertain significance ★★ ⚠ same type
- CYC1 p.Asp209Asn 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/cyc1-p-asp86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown