CKAP2L p.Thr445=
c.1335C>T · rs201537641 · VCV2965061
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00669%, afr)
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 -2 | GERP 0.59 |
| Overall | ||
| CADD | 3.551 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00669%
African / African-American · 5/74,774 alleles
Filtering AF
0.00326%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00294%
Overall
0.00385%
62/1,612,072 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00669% | 14,955 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,599 |
| European (non-Finnish) | 0.00424% | 23,589 |
| South Asian | 0.00331% | 30,193 |
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.Thr445=
- Coding
- c.1335C>T
- MANE Select
- NM_152515
- dbSNP
- rs201537641
- Type
- single nucleotide variant
- Location
- chr2:112756036 (GRCh38)
- Gene constraint
- LOEUF 0.72 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.68
Similar variants
- CKAP2L p.Thr445Ala Uncertain significance ★ ⚠ same residue
- 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
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-thr445 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown