ASPH p.Ala189=
c.567G>A · rs763560642 · VCV1906271
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
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 -1.5 | GERP -3.9 |
| Overall | ||
| CADD | 1.599 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,060 alleles
Filtering AF
0.00307%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00275%
Overall
0.00347%
56/1,613,868 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,765 |
| European (non-Finnish) | 0.00398% | 25,104 |
| Admixed American | 0.00333% | 29,998 |
| African / African-American | 0.00267% | 37,460 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
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
- ASPH
- Protein
- p.Ala189=
- Coding
- c.567G>A
- MANE Select
- NM_004318
- dbSNP
- rs763560642
- Type
- single nucleotide variant
- Location
- chr8:61646802 (GRCh38)
- Gene constraint
- LOEUF 1.011 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 72.34 · 43 PDB
Similar variants
- ASPH p.Ala189Val Likely benign ★ same residue
- ASPH p.Arg735Trp Likely pathogenic ★★ same type
- ASPH p.Tyr565Ter Pathogenic/Likely pathogenic ★★ same type
- ASPH p.Arg425Cys Uncertain significance ★★ ⚠ same type
- ASPH p.Arg753His Uncertain significance ★★ ⚠ same type
- ASPH p.Glu506Val Uncertain significance ★★ same type
- ASPH p.Leu433Arg Uncertain significance ★★ ⚠ same type
- ASPH p.Ser299Asn Uncertain significance ★★ ⚠ same type
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/asph-p-ala189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown