KLF1 p.Pro151=
c.453A>G · rs1326662123 · VCV1915264
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00397%, amr)
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 -1.8 | GERP -3 |
| Overall | ||
| CADD | 11.35 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00397%
Admixed American · 2/50,404 alleles
Filtering AF
0.000658%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000246%
Overall
0.00013%
2/1,539,788 alleles · very rare
exomes 2/1,387,528 · genomes 0/152,260 · joint denominator
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.Pro151=
- Coding
- c.453A>G
- MANE Select
- NM_006563
- dbSNP
- rs1326662123
- Type
- single nucleotide variant
- Location
- chr19:12885777 (GRCh38)
- Gene constraint
- LOEUF 1.777 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.11 · 3 PDB
- Residue 151
- a UniProt-annotated variant site (in cdan4b; likely pathogenic)
Similar variants
- 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
- KLF1 p.Arg328His Uncertain significance ★★ ⚠ same type
- KLF1 p.Arg340His 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-pro151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown