CILK1 p.Phe79=
c.237C>T · rs754954751 · VCV1983257
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0199%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.29 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -5.7 |
| Overall | ||
| CADD | 8.565 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0199%
South Asian · 18/90,504 alleles
Filtering AF
0.0128%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0106%
Overall
0.00168%
27/1,606,004 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0199% | 5,028 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,122 |
| African / African-American | 0.00134% | 74,726 |
| European (non-Finnish) | 0.000596% | 167,742 |
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
- CILK1
- Protein
- p.Phe79=
- Coding
- c.237C>T
- MANE Select
- NM_014920
- dbSNP
- rs754954751
- Type
- single nucleotide variant
- Location
- chr6:53032574 (GRCh38)
- Gene constraint
- LOEUF 0.774 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.47
- Residue 79
- the protein kinase domain
Similar variants
- CILK1 c.1344-4T>A Uncertain significance ★★ same type
- CILK1 p.Ala629Thr Uncertain significance ★★ ⚠ same type
- CILK1 p.Arg124Gln Uncertain significance ★★ ⚠ same type
- CILK1 p.Arg151Gln Uncertain significance ★★ same type
- CILK1 p.Arg262Lys Uncertain significance ★★ ⚠ same type
- CILK1 p.Arg280Gln Uncertain significance ★★ ⚠ same type
- CILK1 p.Arg332Gln Uncertain significance ★★ ⚠ same type
- CILK1 p.Arg475Trp 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/cilk1-p-phe79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown