KL p.Lys342=
c.1026G>A · rs368691338 · VCV1905502
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.8 | GERP 0.063, phastCons 1 |
| Overall | ||
| CADD | 7.833 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,084 alleles
Filtering AF
0.0058%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0026%
Overall
0.00353%
57/1,613,980 alleles · ultra-rare
exomes 52/1,461,836 · genomes 5/152,144 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,042 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,621 |
| African / African-American | 0.00401% | 24,969 |
| European (non-Finnish) | 0.00381% | 26,222 |
| Admixed American | 0.00333% | 29,998 |
| Finnishnot grpmax-eligible | 0.00156% | 64,026 |
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
- KL
- Protein
- p.Lys342=
- Coding
- c.1026G>A
- MANE Select
- NM_004795
- dbSNP
- rs368691338
- Type
- single nucleotide variant
- Location
- chr13:33053973 (GRCh38)
- Gene constraint
- LOEUF 0.917 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.48 · 6 PDB
- Residue 342
- the 'glycosyl hydrolase-1 1' region; an α-helix
Similar variants
- KL c.1331-3C>A Uncertain significance ★★ same type
- KL p.Ala3Thr Uncertain significance ★★ ⚠ same type
- KL p.Ala50Val Uncertain significance ★★ ⚠ same type
- KL p.Ala656Thr Uncertain significance ★★ ⚠ same type
- KL p.Ala663Thr Uncertain significance ★★ ⚠ same type
- KL p.Ala987Thr Uncertain significance ★★ ⚠ same type
- KL p.Arg179Trp Uncertain significance ★★ ⚠ same type
- KL p.Arg181Gln 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/kl-p-lys342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown