AASS p.Lys56=
c.168G>A · rs141727397 · VCV559315
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0394%, nfe)
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 -0.061 | GERP 0.72, phastCons 0.72 |
| Overall | ||
| CADD | 8.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0394%
European (non-Finnish) · 465/1,180,034 alleles
Filtering AF
0.0364%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0352%
Overall
0.0315%
509/1,614,052 alleles · ultra-rare
exomes 477/1,461,892 · genomes 32/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0394% | 2,538 |
| Remaining individualsnot grpmax-eligible | 0.0384% | 2,604 |
| Admixed American | 0.0233% | 4,286 |
| African / African-American | 0.00667% | 14,984 |
| South Asian | 0.0011% | 91,084 |
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
- AASS
- Protein
- p.Lys56=
- Coding
- c.168G>A
- MANE Select
- NM_005763
- dbSNP
- rs141727397
- Type
- single nucleotide variant
- Location
- chr7:122133559 (GRCh38)
- Gene constraint
- LOEUF 0.948 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 90.73 · 9 PDB
- Residue 56
- a modified residue (n6-acetyllysine); the 'lysine-ketoglutarate reductase' region; a β-strand
Similar variants
- AASS c.1767-1G>A Pathogenic/Likely pathogenic ★★ same type
- AASS p.Arg132His Likely pathogenic ★★ same type
- AASS p.Arg132Cys Uncertain significance ★★ ⚠ same type
- AASS p.Arg146Trp Uncertain significance ★★ ⚠ same type
- AASS p.Asn34Lys Uncertain significance ★★ ⚠ same type
- AASS p.Asn865Ser Uncertain significance ★★ ⚠ same type
- AASS p.Gln921Arg Uncertain significance ★★ ⚠ same type
- AASS p.Gly167Cys 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/aass-p-lys56 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown