ASPH p.Leu421=
c.1263G>A · rs138163443 · VCV3037021
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.176%, eas)
Conditions
1
ASPH-related disorder
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 0.63 | GERP 0.14, phastCons 1 |
| Overall | ||
| CADD | 5.599 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.176%
East Asian · 79/44,872 alleles
Filtering AF
0.145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.133%
Overall
0.00539%
87/1,614,046 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.176% | 568 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,929 |
| South Asian | 0.0011% | 91,058 |
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.Leu421=
- Coding
- c.1263G>A
- MANE Select
- NM_004318
- dbSNP
- rs138163443
- Type
- single nucleotide variant
- Location
- chr8:61567205 (GRCh38)
- Gene constraint
- LOEUF 1.011 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 72.34 · 43 PDB
- Residue 421
- an α-helix
Disease context
ASPH-related disorder
Similar variants
- ASPH p.Arg735Trp Likely pathogenic ★★ same condition
- ASPH p.Arg735Gln Likely pathogenic ★ same condition
- ASPH c.977-8T>C Likely benign same condition
- ASPH p.Asp194Asn Likely benign same condition
- ASPH p.His160= Likely benign same condition
- ASPH p.Pro121= Likely benign same condition
- ASPH p.Val214= Likely benign same condition
- ASPH p.Ile497fs 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/asph-p-leu421 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown