KATNB1 p.Pro429=
c.1287G>A · rs569188115 · VCV2185812
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00712%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.8 | GERP -3.2 |
| Overall | ||
| CADD | 0.637 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00712%
European (non-Finnish) · 84/1,180,042 alleles
Filtering AF
0.00588%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00541%
Overall
0.00558%
90/1,614,044 alleles · very rare
exomes 84/1,461,696 · genomes 6/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00712% | 14,048 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,252 |
| African / African-American | 0.00266% | 37,528 |
| Admixed American | 0.00167% | 60,026 |
| Finnishnot grpmax-eligible | 0.00157% | 63,864 |
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.Pro429=
- Coding
- c.1287G>A
- MANE Select
- NM_005886
- dbSNP
- rs569188115
- Type
- single nucleotide variant
- Location
- chr16:57754988 (GRCh38)
- Gene constraint
- LOEUF 0.651 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.58
- Residue 429
- the 'interaction with pafah1b1' 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-pro429 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown