CKAP4 p.His444=
c.1332C>T · rs112234315 · VCV715655
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.65%, 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 -7.8 | GERP -3.8 |
| Overall | ||
| CADD | 0.263 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.65%
African / African-American · 1,235/75,032 alleles
Filtering AF
1.57%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.54%
Overall
0.0862%
1,387/1,608,748 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.65% | 61 |
| Remaining individualsnot grpmax-eligible | 0.0945% | 1,058 |
| Admixed American | 0.0917% | 1,091 |
| Middle Eastern | 0.0331% | 3,024 |
| South Asian | 0.0033% | 30,344 |
| European (non-Finnish) | 0.00271% | 36,861 |
| East Asian | 0.00223% | 44,850 |
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.His444=
- Coding
- c.1332C>T
- MANE Select
- NM_006825
- dbSNP
- rs112234315
- Type
- single nucleotide variant
- Location
- chr12:106239501 (GRCh38)
- Gene constraint
- LOEUF 1.377 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.61
Similar variants
- CKAP4 p.Leu580Val Benign ★★ same type
- CKAP4 p.Thr236= Benign ★★ same type
- CKAP4 p.Tyr483= Likely 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
- CKAP4 p.Ala87Val 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-his444 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown