CKAP5 p.Ser984=
c.2952T>C · rs112595943 · VCV2641754
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.91%, 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 1.1, phastCons 1 |
| Overall | ||
| CADD | 9.356 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.91%
African / African-American · 683/75,062 alleles
Filtering AF
0.853%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.831%
Overall
0.0501%
809/1,614,036 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.91% | 110 |
| Remaining individualsnot grpmax-eligible | 0.0816% | 1,226 |
| Admixed American | 0.075% | 1,334 |
| Middle Eastern | 0.033% | 3,030 |
| South Asian | 0.00329% | 30,356 |
| European (non-Finnish) | 0.00212% | 47,197 |
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
- CKAP5
- Protein
- p.Ser984=
- Coding
- c.2952T>C
- MANE Select
- NM_001008938
- dbSNP
- rs112595943
- Type
- single nucleotide variant
- Location
- chr11:46776294 (GRCh38)
- Gene constraint
- LOEUF 0.143 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.04 · 3 PDB
- Residue 984
- the 'tog 4' region; an α-helix
Similar variants
- CKAP5 c.4569-2A>G Uncertain significance ★ same type
- CKAP5 p.Ala1041Thr Uncertain significance ★ ⚠ same type
- CKAP5 p.Ala1099Thr Uncertain significance ★ ⚠ same type
- CKAP5 p.Ala1127Thr Uncertain significance ★ ⚠ same type
- CKAP5 p.Ala124Ser Uncertain significance ★ ⚠ same type
- CKAP5 p.Ala124Thr Uncertain significance ★ ⚠ same type
- CKAP5 p.Ala1386Ser Uncertain significance ★ ⚠ same type
- CKAP5 p.Ala1429Gly 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/ckap5-p-ser984 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown