KRT6B p.Glu461=
c.1383G>A · VCV3713070
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00801%, 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 0.43 | GERP 0.88, phastCons 1 |
| Overall | ||
| CADD | 7.309 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,940 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00228%
Overall
0.000372%
6/1,614,082 alleles · very rare
exomes 1/1,461,892 · genomes 5/152,190 · 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
- KRT6B
- Protein
- p.Glu461=
- Coding
- c.1383G>A
- MANE Select
- NM_005555
- Type
- single nucleotide variant
- Location
- chr12:52447819 (GRCh38)
- Gene constraint
- LOEUF 0.909 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.76
- Residue 461
- the if rod domain; the 'coil 2' region
Similar variants
- KRT6B p.Glu461Lys Pathogenic/Likely pathogenic ★★ same residue
- 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
- KRT6B p.Gln379Arg 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-glu461 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown