CEP126 p.Leu226=
c.678C>T · rs61742070 · VCV786211
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.33%, afr)
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 0.58 | GERP -4, phastCons 0.87 |
| Overall | ||
| CADD | 6.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.33%
African / African-American · 2,497/74,998 alleles
Filtering AF
3.22%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.18%
Overall
0.175%
2,820/1,613,704 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.33% | 30 |
| Remaining individualsnot grpmax-eligible | 0.211% | 473 |
| Admixed American | 0.165% | 606 |
| Middle Eastern | 0.0827% | 1,209 |
| South Asian | 0.00769% | 13,008 |
| European (non-Finnish) | 0.00678% | 14,748 |
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
- CEP126
- Protein
- p.Leu226=
- Coding
- c.678C>T
- MANE Select
- NM_020802
- dbSNP
- rs61742070
- Type
- single nucleotide variant
- Location
- chr11:101958339 (GRCh38)
- Gene constraint
- LOEUF 0.732 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 49.44
Similar variants
- CEP126 p.Gln146Glu Benign ★★ same type
- CEP126 p.His308Leu Benign ★★ same type
- CEP126 p.Met1021Thr Benign ★★ same type
- CEP126 p.Pro710Ser Benign ★★ same type
- CEP126 p.Ser372Pro Benign ★★ same type
- CEP126 p.Ala1028Thr Uncertain significance ★ ⚠ same type
- CEP126 p.Ala460Val Uncertain significance ★ ⚠ same type
- CEP126 p.Ala607Thr 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/cep126-p-leu226 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown