CKAP2L p.Gln259=
c.777G>A · rs765291620 · VCV747162
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0658%, mid)
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 -0.55 | GERP -2.2, phastCons 0.023 |
| Overall | ||
| CADD | 4.518 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0658%
Middle Eastern · 4/6,076 alleles
Filtering AF
0.0224%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0135%
Overall
0.00136%
22/1,612,992 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0658% | 1,519 |
| Admixed American | 0.0067% | 14,932 |
| African / African-American | 0.00535% | 18,701 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,210 |
| European (non-Finnish) | 0.000678% | 147,467 |
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
- CKAP2L
- Protein
- p.Gln259=
- Coding
- c.777G>A
- MANE Select
- NM_152515
- dbSNP
- rs765291620
- Type
- single nucleotide variant
- Location
- chr2:112756594 (GRCh38)
- Gene constraint
- LOEUF 0.72 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.68
- Residue 259
- the 'disordered' region
Similar variants
- CKAP2L p.Arg206Gly Uncertain significance ★★ ⚠ same type
- CKAP2L p.Arg284Trp Uncertain significance ★★ ⚠ same type
- CKAP2L p.Arg347Lys Uncertain significance ★★ ⚠ same type
- CKAP2L p.Arg688Gln Uncertain significance ★★ ⚠ same type
- CKAP2L p.Cys725Ser Uncertain significance ★★ ⚠ same type
- CKAP2L p.Gln428Arg Uncertain significance ★★ ⚠ same type
- CKAP2L p.Glu462Val Uncertain significance ★★ ⚠ same type
- CKAP2L p.Ile283Leu 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/ckap2l-p-gln259 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown