CYC1 p.Ala150=
c.450G>A · rs780421772 · VCV515732
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0658%, mid)
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 0.59 | GERP -2.4, phastCons 0.99 |
| Overall | ||
| CADD | 8.969 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0658%
Middle Eastern · 4/6,082 alleles
Filtering AF
0.0224%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0184%
Overall
0.0115%
185/1,613,820 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0658% | 1,521 |
| Admixed American | 0.0333% | 2,999 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,165 |
| European (non-Finnish) | 0.0118% | 8,488 |
| South Asian | 0.00549% | 18,216 |
| East Asian | 0.00223% | 44,884 |
| African / African-American | 0.00133% | 74,914 |
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.Ala150=
- Coding
- c.450G>A
- MANE Select
- NM_001916
- dbSNP
- rs780421772
- Type
- single nucleotide variant
- Location
- chr8:144096247 (GRCh38)
- Gene constraint
- LOEUF 0.583 · pLI 0.85 (gnomAD)
- Structure
- AlphaFold pLDDT 86.37 · 5 PDB
- Residue 150
- an α-helix; the cytochrome c domain
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-ala150 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown