KATNB1 p.Pro115=
c.345G>A · rs200282791 · VCV2912532
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -12 | GERP -4.4 |
| Overall | ||
| CADD | 0.349 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00228%
Overall
0.00142%
23/1,614,072 alleles · ultra-rare
exomes 18/1,461,838 · genomes 5/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| Finnishnot grpmax-eligible | 0.0109% | 9,145 |
| African / African-American | 0.008% | 12,502 |
| South Asian | 0.00439% | 22,771 |
| European (non-Finnish) | 0.000424% | 235,999 |
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.Pro115=
- Coding
- c.345G>A
- MANE Select
- NM_005886
- dbSNP
- rs200282791
- Type
- single nucleotide variant
- Location
- chr16:57750882 (GRCh38)
- Gene constraint
- LOEUF 0.651 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.58
- Residue 115
- the 'interaction with centrosomes' region; the 'interaction with dynein' region
Similar variants
- KATNB1 p.Pro115Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown