KRT83 p.Ser450=
c.1350C>T · rs564164020 · VCV2063418
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0214%, afr)
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 -0.084 | GERP -3.7 |
| Overall | ||
| CADD | 3.373 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0214%
African / African-American · 16/74,926 alleles
Filtering AF
0.0133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0109%
Overall
0.00193%
31/1,604,074 alleles · ultra-rare
exomes 25/1,451,726 · genomes 6/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0214% | 4,683 |
| Admixed American | 0.0102% | 9,848 |
| Remaining individualsnot grpmax-eligible | 0.00484% | 20,671 |
| South Asian | 0.00113% | 88,570 |
| European (non-Finnish) | 0.000425% | 235,222 |
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
- KRT83
- Protein
- p.Ser450=
- Coding
- c.1350C>T
- MANE Select
- NM_002282
- dbSNP
- rs564164020
- Type
- single nucleotide variant
- Location
- chr12:52314763 (GRCh38)
- Gene constraint
- LOEUF 1.226 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.81
- Residue 450
- the 'tail' region
Similar variants
- KRT83 p.Glu407Lys Likely pathogenic ★★ same type
- KRT83 p.Arg130Cys Uncertain significance ★★ ⚠ same type
- KRT83 p.Arg168Trp Uncertain significance ★★ ⚠ same type
- KRT83 p.Arg272Gln Uncertain significance ★★ ⚠ same type
- KRT83 p.Arg272Trp Uncertain significance ★★ ⚠ same type
- KRT83 p.Arg293His Uncertain significance ★★ ⚠ same type
- KRT83 p.Arg321Cys Uncertain significance ★★ ⚠ same type
- KRT83 p.Arg321His 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/krt83-p-ser450 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown