CKAP2L p.Ser128=
c.384G>A · rs147582835 · VCV741301
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, 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 -3.2 | GERP -4.8 |
| Overall | ||
| CADD | 2.079 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,062 alleles
Filtering AF
0.0119%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0112%
Overall
0.0118%
190/1,614,176 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,031 |
| Ashkenazi Jewishnot grpmax-eligible | 0.027% | 3,701 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,683 |
| European (non-Finnish) | 0.0136% | 7,329 |
| Admixed American | 0.005% | 20,009 |
| East Asian | 0.00446% | 22,443 |
| South Asian | 0.0022% | 45,545 |
| African / African-American | 0.00133% | 75,032 |
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.Ser128=
- Coding
- c.384G>A
- MANE Select
- NM_152515
- dbSNP
- rs147582835
- Type
- single nucleotide variant
- Location
- chr2:112756987 (GRCh38)
- Gene constraint
- LOEUF 0.72 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.68
- Residue 128
- 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-ser128 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown