CA4 p.Lys232del
c.694_696del · VCV4936267
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 0.97, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,872 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.000124%
2/1,614,144 alleles · very rare
exomes 2/1,461,828 · genomes 0/152,316 · joint denominator
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
- CA4
- Protein
- p.Lys232del
- Coding
- c.694_696del
- MANE Select
- NM_000717
- Type
- Deletion
- Location
- chr17:60158394 (GRCh38)
- Gene constraint
- LOEUF 0.975 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.86 · 10 PDB
- Residue 232
- the alpha-carbonic anhydrase domain
Similar variants
- CA4 p.Lys232Asn Uncertain significance ★★ ⚠ same residue
- CA4 c.415-2_416del Likely pathogenic ★ same type
- CA4 p.Tyr123fs Likely pathogenic ★ same type
- CA4 p.Arg2_Met3del Uncertain significance ★ same type
- CA4 p.Cys305_Ala308del Uncertain significance ★ same type
- CA4 c.112+22del Benign ★ same type
- CA4 c.415-14_415-7del Likely benign ★ same type
- CA4 c.514-15del Likely benign ★ 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/ca4-p-lys232del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown