KATNB1 p.Arg313=
c.939G>C · rs782099693 · VCV2778288
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00246%, 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 1.2 | GERP -0.68, phastCons 0.73 |
| Overall | ||
| CADD | 2.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00246%
European (non-Finnish) · 29/1,179,766 alleles
Filtering AF
0.00172%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00149%
Overall
0.0018%
29/1,610,838 alleles · very rare
exomes 28/1,458,720 · genomes 1/152,118 · 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.Arg313=
- Coding
- c.939G>C
- MANE Select
- NM_005886
- dbSNP
- rs782099693
- Type
- single nucleotide variant
- Location
- chr16:57753160 (GRCh38)
- Gene constraint
- LOEUF 0.651 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.58
- Residue 313
- the 'disordered' region; the 'interaction with pafah1b1' region
Similar variants
- KATNB1 p.Arg313Trp Uncertain significance ★ ⚠ same residue
- KATNB1 p.Arg313Gln Likely benign ★ 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
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-arg313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown