KLC2 p.Arg307=
c.921G>A · rs79498438 · VCV785357
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 7.19%, afr) — too common for a highly-penetrant pathogenic allele
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 0.78 | GERP 0.69, phastCons 1 |
| Overall | ||
| CADD | 7.94 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.19%
African / African-American · 5,395/75,042 alleles
Filtering AF
7.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.96%
Overall
0.373%
6,017/1,614,172 alleles · common
exomes 2,933/1,461,848 · genomes 3,084/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 7.19% | 14 |
| Remaining individualsnot grpmax-eligible | 0.44% | 227 |
| Admixed American | 0.39% | 257 |
| Middle Eastern | 0.214% | 466 |
| South Asian | 0.0154% | 6,507 |
| European (non-Finnish) | 0.00729% | 13,721 |
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
- KLC2
- Protein
- p.Arg307=
- Coding
- c.921G>A
- MANE Select
- NM_001318734
- dbSNP
- rs79498438
- Type
- single nucleotide variant
- Location
- chr11:66263931 (GRCh38)
- Gene constraint
- LOEUF 0.616 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.79 · 2 PDB
- Residue 307
- an α-helix
Similar variants
- KLC2 p.Arg110His Uncertain significance ★★ ⚠ same type
- KLC2 p.Arg418Gln Uncertain significance ★★ ⚠ same type
- KLC2 p.Arg418Trp Uncertain significance ★★ ⚠ same type
- KLC2 p.Arg479His Uncertain significance ★★ ⚠ same type
- KLC2 p.Arg509Gln Uncertain significance ★★ ⚠ same type
- KLC2 p.Arg616Gln Uncertain significance ★★ ⚠ same type
- KLC2 p.Arg96Gln Uncertain significance ★★ same type
- KLC2 p.Asn170Ser 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/klc2-p-arg307 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown