KY p.Lys465=
c.1395G>A · rs376145121 · VCV709140
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.276%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not looked up on this page · why |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.57 | GERP 0.67, phastCons 1 |
| Overall | ||
| CADD | 7.41 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.276%
European (non-Finnish) · 3,252/1,177,880 alleles
Filtering AF
0.268%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.265%
Overall
0.22%
3,549/1,609,584 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.276% | 362 |
| Admixed American | 0.18% | 555 |
| Remaining individualsnot grpmax-eligible | 0.151% | 663 |
| Finnishnot grpmax-eligible | 0.0722% | 1,385 |
| African / African-American | 0.0467% | 2,142 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0407% | 2,459 |
| South Asian | 0.00332% | 30,126 |
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
- KY
- Protein
- p.Lys465=
- Coding
- c.1395G>A
- MANE Select
- NM_001353108 · reported on NM_178554
- dbSNP
- rs376145121
- Type
- single nucleotide variant
- Location
- chr3:134604170 (GRCh38)
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/ky-p-lys465 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown