KRT6B p.Ser60=
c.180T>C · rs747994676 · VCV3037279
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.237%, eas)
Conditions
1
KRT6B-related disorder
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 -1.5 | GERP -1.4 |
| Overall | ||
| CADD | 8.539 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.237%
East Asian · 70/29,576 alleles
Filtering AF
0.192%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.176%
Overall
0.0299%
438/1,464,920 alleles · rare
exomes 101/1,335,258 · genomes 337/129,662 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.237% | 423 |
| Admixed American | 0.0644% | 1,552 |
| Finnishnot grpmax-eligible | 0.0507% | 1,971 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0465% | 2,150 |
| Middle Eastern | 0.0236% | 4,234 |
| European (non-Finnish) | 0.0229% | 4,362 |
| African / African-American | 0.0219% | 4,560 |
| South Asian | 0.0208% | 4,808 |
| Remaining individualsnot grpmax-eligible | 0.0178% | 5,619 |
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.Ser60=
- Coding
- c.180T>C
- MANE Select
- NM_005555
- dbSNP
- rs747994676
- Type
- single nucleotide variant
- Location
- chr12:52451899 (GRCh38)
- Gene constraint
- LOEUF 0.909 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.76
- Residue 60
- the 'head' region
Disease context
KRT6B-related disorder
Similar variants
- KRT6B p.Gly66= Likely benign same condition
- KRT6B p.Gly88Arg Benign same condition
- KRT6B p.Leu61= Likely benign same condition
- KRT6B p.Pro128= Benign same condition
- KRT6B p.Pro154= Likely benign same condition
- KRT6B p.Ser67= Likely benign same condition
- KRT6B p.Asn172del Pathogenic ★★ same condition
- KRT6B p.Glu461Lys Pathogenic/Likely pathogenic ★★ 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-ser60 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown