CDYL2 p.Thr261=
c.783G>A · rs148307202 · VCV784661
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.88%, 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 -8.6 | GERP -3.4 |
| Overall | ||
| CADD | 3.925 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.88%
African / African-American · 2,161/75,022 alleles
Filtering AF
2.78%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.74%
Overall
0.158%
2,546/1,614,142 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.88% | 35 |
| Middle Eastern | 0.28% | 357 |
| Admixed American | 0.228% | 438 |
| Remaining individualsnot grpmax-eligible | 0.203% | 492 |
| South Asian | 0.0132% | 7,590 |
| European (non-Finnish) | 0.0078% | 12,826 |
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
- CDYL2
- Protein
- p.Thr261=
- Coding
- c.783G>A
- MANE Select
- NM_152342
- dbSNP
- rs148307202
- Type
- single nucleotide variant
- Location
- chr16:80633070 (GRCh38)
- Gene constraint
- LOEUF 0.713 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.08 · 8 PDB
Similar variants
- CDYL2 p.Gly355= Benign ★★ same type
- CDYL2 p.Ala114Gly Uncertain significance ★ ⚠ same type
- CDYL2 p.Ala114Thr Uncertain significance ★ ⚠ same type
- CDYL2 p.Ala286Val Uncertain significance ★ ⚠ same type
- CDYL2 p.Ala334Thr Uncertain significance ★ ⚠ same type
- CDYL2 p.Ala341Gly Uncertain significance ★ ⚠ same type
- CDYL2 p.Ala362Thr Uncertain significance ★ ⚠ same type
- CDYL2 p.Ala384Thr 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/cdyl2-p-thr261 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown