KRT6B p.Lys438=
c.1314G>A · VCV4820777
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0227%, afr)
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 -0.25 | GERP 0.88 |
| Overall | ||
| CADD | 8.931 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0227%
African / African-American · 17/74,892 alleles
Filtering AF
0.0144%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0119%
Overall
0.00752%
121/1,608,140 alleles · ultra-rare
exomes 108/1,455,856 · genomes 13/152,284 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0227% | 4,405 |
| Admixed American | 0.00834% | 11,986 |
| European (non-Finnish) | 0.00766% | 13,053 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,770 |
| Finnishnot grpmax-eligible | 0.00469% | 21,330 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00339% | 29,542 |
| East Asian | 0.00223% | 44,824 |
| South Asian | 0.0011% | 90,960 |
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
- KRT6B
- Protein
- p.Lys438=
- Coding
- c.1314G>A
- MANE Select
- NM_005555
- Type
- single nucleotide variant
- Location
- chr12:52447888 (GRCh38)
- Gene constraint
- LOEUF 0.909 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.76
- Residue 438
- the if rod domain; the 'coil 2' region
Similar variants
- KRT6B p.Lys438Arg Likely benign ★★ ⚠ same residue
- KRT6B p.Glu461Lys Pathogenic/Likely pathogenic ★★ same type
- KRT6B p.Glu472Lys Pathogenic ★★ same type
- KRT6B p.Ala403Val Uncertain significance ★★ ⚠ same type
- KRT6B p.Arg260His Uncertain significance ★★ same type
- KRT6B p.Arg375His Uncertain significance ★★ ⚠ same type
- KRT6B p.Arg386His Uncertain significance ★★ same type
- KRT6B p.Gln208His 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/krt6b-p-lys438 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown