KATNB1 p.Pro233=
c.699C>A · rs34508238 · VCV733926
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.449%, 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 -5.3 | GERP -3 |
| Overall | ||
| CADD | 0.494 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.449%
African / African-American · 334/74,346 alleles
Filtering AF
0.409%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.394%
Overall
0.0236%
370/1,565,802 alleles · rare
exomes 173/1,413,494 · genomes 197/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.449% | 223 |
| Remaining individualsnot grpmax-eligible | 0.0329% | 3,037 |
| Admixed American | 0.023% | 4,339 |
| Middle Eastern | 0.0167% | 6,002 |
| South Asian | 0.00235% | 42,597 |
| European (non-Finnish) | 8.66e-05% | 1,155,168 |
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
- KATNB1
- Protein
- p.Pro233=
- Coding
- c.699C>A
- MANE Select
- NM_005886
- dbSNP
- rs34508238
- Type
- single nucleotide variant
- Location
- chr16:57752596 (GRCh38)
- Gene constraint
- LOEUF 0.651 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.58
- Residue 233
- the 'interaction with centrosomes' region; the 'interaction with dynein' region
Similar variants
- KATNB1 c.1416+1G>A Likely pathogenic ★★ same type
- KATNB1 p.Ala121Val Uncertain significance ★★ ⚠ same type
- KATNB1 p.Ala163Val Uncertain significance ★★ ⚠ same type
- KATNB1 p.Ala411Thr Uncertain significance ★★ ⚠ same type
- KATNB1 p.Ala453Val Uncertain significance ★★ ⚠ same type
- KATNB1 p.Ala652Asp Uncertain significance ★★ ⚠ same type
- KATNB1 p.Arg304Cys Uncertain significance ★★ ⚠ same type
- KATNB1 p.Arg34Gln 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/katnb1-p-pro233 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown