CKAP4 p.Tyr483=
c.1449C>T · rs145284636 · VCV715809
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.274%, nfe)
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 0.13 | GERP -1.1 |
| Overall | ||
| CADD | 4.853 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.274%
European (non-Finnish) · 3,226/1,178,138 alleles
Filtering AF
0.266%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.263%
Overall
0.215%
3,439/1,601,422 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.274% | 365 |
| Remaining individualsnot grpmax-eligible | 0.196% | 510 |
| Admixed American | 0.075% | 1,333 |
| African / African-American | 0.052% | 1,924 |
| Finnishnot grpmax-eligible | 0.00559% | 17,879 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,580 |
| South Asian | 0.00329% | 30,351 |
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
- CKAP4
- Protein
- p.Tyr483=
- Coding
- c.1449C>T
- MANE Select
- NM_006825
- dbSNP
- rs145284636
- Type
- single nucleotide variant
- Location
- chr12:106239384 (GRCh38)
- Gene constraint
- LOEUF 1.377 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.61
Similar variants
- CKAP4 p.Tyr483Cys Uncertain significance ★ ⚠ same residue
- CKAP4 p.His444= Benign ★★ same type
- CKAP4 p.Leu580Val Benign ★★ same type
- CKAP4 p.Thr236= Benign ★★ same type
- CKAP4 p.Ala167Gly Uncertain significance ★ ⚠ same type
- CKAP4 p.Ala23Gly Uncertain significance ★ ⚠ same type
- CKAP4 p.Ala449Thr Uncertain significance ★ ⚠ same type
- CKAP4 p.Ala522Thr 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/ckap4-p-tyr483 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown