CYC1 p.Val11=
c.33A>G · rs897714161 · VCV506457
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0491%, 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 -1.8 | GERP -2.5 |
| Overall | ||
| CADD | 8.328 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0491%
European (non-Finnish) · 477/972,074 alleles
Filtering AF
0.0454%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.044%
Overall
0.0416%
503/1,208,974 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0491% | 2,038 |
| Remaining individualsnot grpmax-eligible | 0.0296% | 3,375 |
| Admixed American | 0.0263% | 3,797 |
| African / African-American | 0.011% | 9,057 |
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.Val11=
- Coding
- c.33A>G
- MANE Select
- NM_001916
- dbSNP
- rs897714161
- Type
- single nucleotide variant
- Location
- chr8:144095132 (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-val11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown