KLF10 p.Ser140=
c.420C>T · rs147912564 · VCV2068861
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, 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 0.001 | GERP -0.53 |
| Overall | ||
| CADD | 6.094 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
African / African-American · 15/74,994 alleles
Filtering AF
0.0123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00988%
Overall
0.000991%
16/1,614,042 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.02% | 5,000 |
| Finnishnot grpmax-eligible | 0.00156% | 63,988 |
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.Ser140=
- Coding
- c.420C>T
- MANE Select
- NM_005655
- dbSNP
- rs147912564
- Type
- single nucleotide variant
- Location
- chr8:102651912 (GRCh38)
- Gene constraint
- LOEUF 0.817 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.62 · 1 PDB
Similar variants
- KLF10 p.Ser140Arg Uncertain significance ★★ ⚠ same residue
- 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
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-ser140 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown