KLF11 p.Pro4=
c.12G>A · rs1463894217 · VCV1625144
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00268%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Overall | ||
| CADD | 6.776 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00268%
European (non-Finnish) · 28/1,045,728 alleles
Filtering AF
0.00186%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0016%
Overall
0.00226%
31/1,369,364 alleles · very rare
exomes 31/1,220,232 · genomes 0/149,132 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00268% | 37,347 |
| Remaining individualsnot grpmax-eligible | 0.00204% | 48,958 |
| African / African-American | 0.00155% | 64,722 |
| South Asian | 0.00127% | 78,540 |
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
- KLF11
- Protein
- p.Pro4=
- Coding
- c.12G>A
- MANE Select
- NM_003597
- dbSNP
- rs1463894217
- Type
- single nucleotide variant
- Location
- chr2:10043728 (GRCh38)
- Gene constraint
- LOEUF 1.07 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 49.73
Similar variants
- KLF11 c.-104C>T Uncertain significance ★★ same type
- KLF11 p.Ala146Val Uncertain significance ★★ ⚠ same type
- KLF11 p.Ala321Pro Uncertain significance ★★ ⚠ same type
- KLF11 p.Ala89Val Uncertain significance ★★ ⚠ same type
- KLF11 p.Arg120Gly Uncertain significance ★★ ⚠ same type
- KLF11 p.Arg390Gln Uncertain significance ★★ same type
- KLF11 p.Arg402Trp Uncertain significance ★★ ⚠ same type
- KLF11 p.Arg474Gln 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/klf11-p-pro4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown