CYC1 p.Phe172=
c.516C>T · rs763149418 · VCV1940739
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.41 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.26 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -6.8 | GERP -3.1 |
| Overall | ||
| CADD | 10.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,996 alleles
Overall
6.84e-05%
1/1,461,874 alleles · very rare
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.Phe172=
- Coding
- c.516C>T
- MANE Select
- NM_001916
- dbSNP
- rs763149418
- Type
- single nucleotide variant
- Location
- chr8:144096399 (GRCh38)
- Gene constraint
- LOEUF 0.583 · pLI 0.85 (gnomAD)
- Structure
- AlphaFold pLDDT 86.37 · 5 PDB
- Residue 172
- 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-phe172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown