CDKN1C p.186AP[9]
c.573GGCCCC[3] · rs759134767 · VCV236967
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.52%, amr)
Conditions
2
Beckwith-Wiedemann syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.34 | GERP -1 |
| Overall | ||
| CADD | 10.9 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | G-rich low complexity, simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.52%
Admixed American · 658/18,682 alleles
Filtering AF
3.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.21%
Overall
0.153%
1,562/1,022,866 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 3.52% | 28 |
| Middle Eastern | 0.416% | 240 |
| African / African-American | 0.339% | 295 |
| South Asian | 0.217% | 460 |
| Remaining individualsnot grpmax-eligible | 0.156% | 642 |
| European (non-Finnish) | 0.0714% | 1,401 |
| Finnishnot grpmax-eligible | 0.0193% | 5,176 |
| East Asian | 0.00494% | 20,244 |
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
- CDKN1C
- Protein
- p.186AP[9]
- Coding
- c.573GGCCCC[3]
- MANE Select
- NM_001122630
- dbSNP
- rs759134767
- Type
- Indel
- Location
- chr11:2884861 (GRCh38)
- Gene constraint
- LOEUF 1.943 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 63.93
Similar variants
- CDKN1C p.Ala185Leu Uncertain significance ★★ same condition
- CDKN1C p.Arg222Gln Uncertain significance ★★ same condition
- CDKN1C p.Glu30Leu Uncertain significance ★★ same condition
- CDKN1C p.186_187AP[12] Benign/Likely benign ★★ same condition
- CDKN1C p.186_187AP[15] Likely benign ★★ same condition
- CDKN1C p.186_187AP[7] Benign/Likely benign ★★ same condition
- CDKN1C p.186_187AP[8] Benign/Likely benign ★★ same condition
- CDKN1C p.Ala202fs Pathogenic ★ same condition
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/cdkn1c-p-186ap-9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown