KLF6 p.Ser77=
c.231C>T · rs35835052 · VCV717974
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.97%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.083 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -8.6 | GERP -2.9 |
| Overall | ||
| CADD | 0.554 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.97%
African / African-American · 3,725/74,976 alleles
Filtering AF
4.84%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.78%
Overall
0.274%
4,417/1,614,020 alleles · low-frequency
exomes 2,226/1,461,822 · genomes 2,191/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.97% | 20 |
| Admixed American | 0.448% | 223 |
| Middle Eastern | 0.396% | 253 |
| Remaining individualsnot grpmax-eligible | 0.395% | 253 |
| South Asian | 0.0154% | 6,505 |
| European (non-Finnish) | 0.0115% | 8,676 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,602 |
| East Asian | 0.00223% | 44,884 |
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
- KLF6
- Protein
- p.Ser77=
- Coding
- c.231C>T
- MANE Select
- NM_001300
- dbSNP
- rs35835052
- Type
- single nucleotide variant
- Location
- chr10:3782086 (GRCh38)
- Gene constraint
- LOEUF 0.108 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 59.24
Similar variants
- KLF6 p.Arg201= Benign/Likely benign ★★ same type
- KLF6 p.Val165Met Benign ★★ same type
- KLF6 p.Arg156Lys Uncertain significance ★ ⚠ same type
- KLF6 p.Arg201Trp Uncertain significance ★ ⚠ same type
- KLF6 p.Asp190Tyr Uncertain significance ★ same type
- KLF6 p.Gly178Glu Uncertain significance ★ ⚠ same type
- KLF6 p.Ile68Met Uncertain significance ★ ⚠ same type
- KLF6 p.Leu13Val 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/klf6-p-ser77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown