KLF1 p.Pro107=
c.321G>T · VCV3615012
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00137%, 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 |
|---|---|---|
| Pangolin | Δ0.21 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP -2.6 | GERP -3 |
| Overall | ||
| CADD | 5.542 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00137%
African / African-American · 1/73,154 alleles
Filtering AF
7e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000258%
4/1,551,730 alleles · very rare
exomes 4/1,399,370 · genomes 0/152,360 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00137% | 73,154 |
| European (non-Finnish) | 0.000261% | 382,573 |
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
- KLF1
- Protein
- p.Pro107=
- Coding
- c.321G>T
- MANE Select
- NM_006563
- Type
- single nucleotide variant
- Location
- chr19:12885909 (GRCh38)
- Gene constraint
- LOEUF 1.777 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.11 · 3 PDB
- Residue 107
- a UniProt-annotated variant site (in cdan4b; likely pathogenic); the 'disordered' region
Similar variants
- KLF1 p.Pro107Leu Uncertain significance ★★ ⚠ same residue
- KLF1 p.Pro107Ser Uncertain significance ★ ⚠ same residue
- KLF1 p.Ala298Pro Pathogenic ★★ same type
- KLF1 c.*263C>T Uncertain significance ★★ same type
- KLF1 p.Ala142Val Uncertain significance ★★ ⚠ same type
- KLF1 p.Ala165Ser Uncertain significance ★★ ⚠ same type
- KLF1 p.Ala262Ser Uncertain significance ★★ ⚠ same type
- KLF1 p.Arg137Cys 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/klf1-p-pro107 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown