NPC2 p.Lys94=
c.282G>A · rs2506104474 · VCV1796572
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.114 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.84 | GERP -0.29, phastCons 0.88 |
| Overall | ||
| CADD | 8.321 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- NPC2
- Protein
- p.Lys94=
- Coding
- c.282G>A
- MANE Select
- NM_006432
- dbSNP
- rs2506104474
- Type
- single nucleotide variant
- Location
- chr14:74484496 (GRCh38)
- Gene constraint
- LOEUF 1.422 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.88 · 2 PDB
- Residue 94
- an α-helix
Similar variants
- NPC2 p.Lys94Glu Uncertain significance ★ ⚠ same residue
- NPC2 p.Cys47Ter Pathogenic ★★ same condition
- NPC2 p.Glu20Ter Pathogenic ★★ same condition
- NPC2 p.Lys94Ter Pathogenic/Likely pathogenic ★★ same residue
- NPC2 p.Asn98His Uncertain significance ★★ ⚠ same condition
- NPC2 p.Asp91Asn Uncertain significance ★★ ⚠ same condition
- NPC2 p.Gln102Arg Uncertain significance ★★ ⚠ same condition
- NPC2 p.Gln136Glu Uncertain significance ★★ ⚠ same condition
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/npc2-p-lys94 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown