CKAP2L p.Val256=
c.768A>G · rs17042342 · VCV1273625
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 18.1%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.87 | GERP -4.9 |
| Overall | ||
| CADD | 1.514 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
18.1%
African / African-American · 13,544/74,800 alleles
Filtering AF
17.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 17.7%
Overall
5.22%
84,113/1,612,690 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 18.1% | 6 |
| Remaining individualsnot grpmax-eligible | 5.44% | 18 |
| European (non-Finnish) | 5.09% | 20 |
| Middle Eastern | 5.07% | 20 |
| Admixed American | 3.95% | 25 |
| Ashkenazi Jewishnot grpmax-eligible | 3.77% | 27 |
| South Asian | 2.27% | 44 |
| Finnishnot grpmax-eligible | 2.11% | 47 |
| Amishnot grpmax-eligible | 0.33% | 303 |
| East Asian | 0.00891% | 11,222 |
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.Val256=
- Coding
- c.768A>G
- MANE Select
- NM_152515
- dbSNP
- rs17042342
- Type
- single nucleotide variant
- Location
- chr2:112756603 (GRCh38)
- Gene constraint
- LOEUF 0.72 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.68
- Residue 256
- 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-val256 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown