KLF10 p.Pro201=
c.603A>G · rs139430867 · VCV1592840
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.157%, 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 -0.59 | GERP -4, phastCons 0.001 |
| Overall | ||
| CADD | 5.161 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.157%
African / African-American · 118/75,064 alleles
Filtering AF
0.134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.125%
Overall
0.00954%
154/1,614,236 alleles · rare
exomes 80/1,461,890 · genomes 74/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.157% | 636 |
| Middle Eastern | 0.033% | 3,031 |
| Admixed American | 0.025% | 4,002 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,946 |
| South Asian | 0.00329% | 30,361 |
| European (non-Finnish) | 0.000593% | 168,577 |
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.Pro201=
- Coding
- c.603A>G
- MANE Select
- NM_005655
- dbSNP
- rs139430867
- Type
- single nucleotide variant
- Location
- chr8:102651729 (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-pro201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown