KLF10 p.Phe307=
c.921C>T · rs1433658976 · VCV1533729
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00334%, amr)
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 5.9 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 10.76 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00334%
Admixed American · 2/59,864 alleles
Filtering AF
0.000554%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.00031%
5/1,612,360 alleles · very rare
exomes 3/1,460,200 · genomes 2/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00334% | 29,932 |
| European (non-Finnish) | 0.000254% | 393,034 |
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
- KLF10
- Protein
- p.Phe307=
- Coding
- c.921C>T
- MANE Select
- NM_005655
- dbSNP
- rs1433658976
- Type
- single nucleotide variant
- Location
- chr8:102651411 (GRCh38)
- Gene constraint
- LOEUF 0.817 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.62 · 1 PDB
Similar variants
- KLF10 p.Ala111Val Uncertain significance ★★ ⚠ same type
- KLF10 p.Ala113Pro Uncertain significance ★★ ⚠ same type
- KLF10 p.Ala132Thr Uncertain significance ★★ ⚠ same type
- KLF10 p.Ala203Ser Uncertain significance ★★ ⚠ same type
- KLF10 p.Ala316Thr Uncertain significance ★★ ⚠ same type
- KLF10 p.Ala354Val Uncertain significance ★★ ⚠ same type
- KLF10 p.Ala355Ser Uncertain significance ★★ ⚠ same type
- KLF10 p.Ala430Thr 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/klf10-p-phe307 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown