CKAP2 p.Thr312=
c.936T>A · rs74085795 · VCV790677
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.97%, 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 -0.063 | GERP -3.6 |
| Overall | ||
| CADD | 0.671 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.97%
African / African-American · 2,229/75,014 alleles
Filtering AF
2.87%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.83%
Overall
0.171%
2,762/1,613,842 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.97% | 34 |
| Middle Eastern | 0.297% | 337 |
| Remaining individualsnot grpmax-eligible | 0.234% | 428 |
| Admixed American | 0.218% | 458 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0372% | 2,691 |
| European (non-Finnish) | 0.0183% | 5,462 |
| South Asian | 0.0121% | 8,277 |
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
- CKAP2
- Protein
- p.Thr312=
- Coding
- c.936T>A
- MANE Select
- NM_018204
- dbSNP
- rs74085795
- Type
- single nucleotide variant
- Location
- chr13:52461762 (GRCh38)
- Gene constraint
- LOEUF 0.983 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 59.29
Similar variants
- CKAP2 p.Arg628Gln Uncertain significance ★★ ⚠ same type
- CKAP2 p.Asn386Asp Benign ★★ same type
- CKAP2 p.Ala214Ser Uncertain significance ★ ⚠ same type
- CKAP2 p.Ala326Thr Uncertain significance ★ ⚠ same type
- CKAP2 p.Ala347Ser Uncertain significance ★ ⚠ same type
- CKAP2 p.Ala350Thr Uncertain significance ★ ⚠ same type
- CKAP2 p.Ala614Ser Uncertain significance ★ ⚠ same type
- CKAP2 p.Ala614Thr 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/ckap2-p-thr312 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown