LYST p.Ala554=
c.1662C>A · rs2527112050 · VCV2911812
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
Chediak-Higashi syndrome
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 -3.9 | GERP -4.3 |
| Overall | ||
| CADD | 0.04 | 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
- LYST
- Protein
- p.Ala554=
- Coding
- c.1662C>A
- MANE Select
- NM_000081
- dbSNP
- rs2527112050
- Type
- single nucleotide variant
- Location
- chr1:235809156 (GRCh38)
- Gene constraint
- LOEUF 0.505 · pLI <0.01 (gnomAD)
Disease context
Chediak-Higashi syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Chédiak-Higashi syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood
Similar variants
- LYST p.Ala554Val Uncertain significance ★ ⚠ same residue
- LYST c.192+1G>A Pathogenic/Likely pathogenic ★★ same condition
- LYST c.4862+2T>A Likely pathogenic ★★ same condition
- LYST c.4863-1G>C Likely pathogenic ★★ same condition
- LYST c.6882-1G>T Likely pathogenic ★★ same condition
- LYST c.8358+2T>C Pathogenic/Likely pathogenic ★★ same condition
- LYST c.8358+2T>G Likely pathogenic ★★ same condition
- LYST c.8802-2A>G Pathogenic/Likely pathogenic ★★ 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/lyst-p-ala554 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown