ALAS2 p.Pro520=
c.1560C>A · rs150055592 · VCV214089
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 0.027 | GERP -3.3, phastCons 0.38 |
| Overall | ||
| CADD | 5.321 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Amishnot grpmax-eligible | 1.6% | 62 |
| Middle Easterngrpmax | 0.804% | 124 |
| Ashkenazi Jewishnot grpmax-eligible | 0.654% | 153 |
| Finnishnot grpmax-eligible | 0.611% | 164 |
| Remaining individualsnot grpmax-eligible | 0.456% | 219 |
| European (non-Finnish) | 0.419% | 239 |
| Admixed American | 0.363% | 275 |
| South Asian | 0.0776% | 1,289 |
| African / African-American | 0.0385% | 2,597 |
Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- ALAS2
- Protein
- p.Pro520=
- Coding
- c.1560C>A
- MANE Select
- NM_000032
- dbSNP
- rs150055592
- Type
- single nucleotide variant
- Location
- chrX:55013526 (GRCh38)
- Structure
- AlphaFold pLDDT 82.76 · 27 PDB
- Residue 520
- a UniProt-annotated variant site (in sidba1; likely benign; associated in cis with h-560 in a patient)
Disease context
X-linked sideroblastic anemia 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor X-linked sideroblastic anemia (Orphanet):
- Inheritance
- X-linked recessive
- Onset
- All ages
Similar variants
- ALAS2 p.Pro520Leu Benign/Likely benign ★★ same residue
- ALAS2 p.Arg411Cys Pathogenic ★★ same condition
- ALAS2 p.Arg452Cys Pathogenic ★★ ⚠ same condition
- ALAS2 p.Ala336Asp Uncertain significance ★★ ⚠ same condition
- ALAS2 p.Cys471Arg Uncertain significance ★★ ⚠ same condition
- ALAS2 c.824-15C>T Benign ★★ same condition
- ALAS2 c.*124C>T Benign/Likely benign ★★ same condition
- ALAS2 c.*56A>C Benign ★★ 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/alas2-p-pro520 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown