LYST p.Asp15=
c.45T>C · rs1675833748 · VCV1694320
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
Conditions
2
autoinflammatory 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 0.35 | GERP -3.1, phastCons 0.43 |
| Overall | ||
| CADD | 3.781 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,040 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000248%
4/1,613,732 alleles · very rare
exomes 3/1,461,622 · genomes 1/152,110 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,520 |
| European (non-Finnish) | 0.00017% | 589,957 |
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
- LYST
- Protein
- p.Asp15=
- Coding
- c.45T>C
- MANE Select
- NM_000081
- dbSNP
- rs1675833748
- Type
- single nucleotide variant
- Location
- chr1:235830373 (GRCh38)
- Gene constraint
- LOEUF 0.505 · pLI <0.01 (gnomAD)
Similar variants
- LYST p.Asp15Asn 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-asp15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown