CDK6 p.Ser156=
c.468C>T · VCV4872351
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.52 | GERP -4.2 |
| Overall | ||
| CADD | 8.831 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,888 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000558%
9/1,613,974 alleles · very rare
exomes 8/1,461,770 · genomes 1/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,963 |
| South Asian | 0.0022% | 45,542 |
| Admixed American | 0.00167% | 59,986 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| European (non-Finnish) | 0.000169% | 589,991 |
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
- CDK6
- Protein
- p.Ser156=
- Coding
- c.468C>T
- MANE Select
- NM_001145306
- Type
- single nucleotide variant
- Location
- chr7:92725695 (GRCh38)
- Gene constraint
- LOEUF 0.412 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 85.81 · 22 PDB
- Residue 156
- the protein kinase domain
Similar variants
- CDK6 c.370-118G>A Benign ★★ same type
- CDK6 c.537+257A>T Benign ★★ same type
- CDK6 c.538-14G>A Benign ★★ same type
- CDK6 c.647+153C>T Benign ★★ same type
- CDK6 c.698+147G>C Benign ★★ same type
- CDK6 c.699-18T>C Benign ★★ same type
- CDK6 c.834+53T>C Benign ★★ same type
- CDK6 c.*32G>A Benign ★★ 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/cdk6-p-ser156 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown