ASXL1 p.Ser201=
c.603C>T · rs2123222993 · VCV2824100
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Conditions
1
Inborn genetic diseases
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 2.6 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 11.35 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,504 alleles
Overall
6.87e-05%
1/1,455,744 alleles · very rare
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
- ASXL1
- Protein
- p.Ser201=
- Coding
- c.603C>T
- MANE Select
- NM_015338
- dbSNP
- rs2123222993
- Type
- single nucleotide variant
- Location
- chr20:32429938 (GRCh38)
- Gene constraint
- LOEUF 0.918 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 42.74 · 4 PDB
- Residue 201
- the 'disordered' region
Similar variants
- ASXL1 p.Ser201Gly Uncertain significance ★★ ⚠ same residue
- ASXL1 p.Arg1415Ter Pathogenic ★★ same condition
- ASXL1 p.Arg143Ter Pathogenic/Likely pathogenic ★★ same condition
- ASXL1 p.Ala1002Asp Uncertain significance ★★ ⚠ same condition
- ASXL1 p.Ala1002Pro Uncertain significance ★★ ⚠ same condition
- ASXL1 p.Ala1041Val Uncertain significance ★★ ⚠ same condition
- ASXL1 p.Ala1172Val Uncertain significance ★★ ⚠ same condition
- ASXL1 p.Ala1199Thr Uncertain significance ★★ ⚠ 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/asxl1-p-ser201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown