CKAP4 p.Thr236=
c.708G>A · rs141436009 · VCV735481
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.92%, sas)
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 -7.4 | GERP -4 |
| Overall | ||
| CADD | 2.802 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.92%
South Asian · 1,745/91,080 alleles
Filtering AF
1.84%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.81%
Overall
0.119%
1,917/1,614,204 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.92% | 52 |
| Remaining individualsnot grpmax-eligible | 0.126% | 791 |
| Middle Eastern | 0.066% | 1,516 |
| European (non-Finnish) | 0.00669% | 14,937 |
| East Asian | 0.00669% | 14,959 |
| African / African-American | 0.00666% | 15,012 |
| Admixed American | 0.00333% | 30,016 |
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.Thr236=
- Coding
- c.708G>A
- MANE Select
- NM_006825
- dbSNP
- rs141436009
- Type
- single nucleotide variant
- Location
- chr12:106240125 (GRCh38)
- Gene constraint
- LOEUF 1.377 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.61
Similar variants
- CKAP4 p.His444= Benign ★★ same type
- CKAP4 p.Leu580Val 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-thr236 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown