YTHDF1 p.Asp53Glu
c.159C>A · VCV4606268
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.4467 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
0/2 damaging
REVEL, SaProt · AlphaMissense indeterminate
Computational evidence
| Protein change | ||
| AlphaMissense | 0.4467 | ambiguous |
|---|---|---|
| REVEL | 0.186 | benign-leaning |
| SaProt | LLR -7.43 | tolerated |
| ⇒ REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.65 | GERP -4.3 |
| Regional constraint | o/e 0.95 | unconstrained · MANE · 13 kb · p 0.25 · regional, not allelic |
| Overall | ||
| CADD | 13.17 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- YTHDF1
- Protein
- p.Asp53Glu
- Coding
- c.159C>A
- MANE Select
- NM_017798
- Type
- single nucleotide variant
- Location
- chr20:63203781 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI 0.96 (gnomAD)
- Structure
- AlphaFold pLDDT 62.83 · 10 PDB
Similar variants
- YTHDF1 p.Asn497= Benign ★★ same type
- YTHDF1 p.His375Tyr Benign ★★ same type
- YTHDF1 p.Lys473= Benign ★★ same type
- YTHDF1 p.Ser145= Benign ★★ same type
- YTHDF1 p.Ser252= Benign ★★ same type
- YTHDF1 p.Val195= Benign ★★ same type
- YTHDF1 p.Ala146Thr Uncertain significance ★ ⚠ same type
- YTHDF1 p.Ala199Ser 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/ythdf1-p-asp53glu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown