KATNB1 p.Pro340=
c.1020C>G · VCV3682020
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000511%, nfe)
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 -0.36 | GERP 0.49, phastCons 0.082 |
| Overall | ||
| CADD | 8.074 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000511%
European (non-Finnish) · 6/1,174,706 alleles
Filtering AF
0.000184%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000121%
Overall
0.000374%
6/1,602,380 alleles · very rare
exomes 5/1,450,184 · genomes 1/152,196 · 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
- KATNB1
- Protein
- p.Pro340=
- Coding
- c.1020C>G
- MANE Select
- NM_005886
- Type
- single nucleotide variant
- Location
- chr16:57753241 (GRCh38)
- Gene constraint
- LOEUF 0.651 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.58
- Residue 340
- the 'disordered' region; the 'interaction with pafah1b1' region
Similar variants
- KATNB1 p.Pro340Leu 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-pro340 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown