KLF11 p.Pro71=
c.213C>T · VCV4953337
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0657%, mid)
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 -0.71 | GERP -1.6, phastCons 0.006 |
| Overall | ||
| CADD | 7.736 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0657%
Middle Eastern · 4/6,084 alleles
Filtering AF
0.0224%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0135%
Overall
0.00316%
51/1,614,060 alleles · ultra-rare
exomes 49/1,461,886 · genomes 2/152,174 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0657% | 1,521 |
| European (non-Finnish) | 0.00347% | 28,782 |
| South Asian | 0.00329% | 30,363 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
| East Asian | 0.00223% | 44,900 |
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.Pro71=
- Coding
- c.213C>T
- MANE Select
- NM_003597
- Type
- single nucleotide variant
- Location
- chr2:10046320 (GRCh38)
- Gene constraint
- LOEUF 1.07 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 49.73
Similar variants
- KLF11 p.Pro71Ala Uncertain significance ★ same residue
- KLF11 p.Pro71Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown