YTHDF1 p.Lys473=
c.1419G>A · rs144959355 · VCV720629
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.9%, afr)
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 0.78 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 5.847 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.9%
African / African-American · 1,430/75,080 alleles
Filtering AF
1.82%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.79%
Overall
0.117%
1,892/1,614,238 alleles · low-frequency
exomes 1,059/1,461,848 · genomes 833/152,390 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.9% | 53 |
| Ashkenazi Jewishnot grpmax-eligible | 0.578% | 173 |
| Remaining individualsnot grpmax-eligible | 0.195% | 512 |
| Admixed American | 0.115% | 870 |
| Middle Eastern | 0.099% | 1,010 |
| South Asian | 0.0351% | 2,847 |
| European (non-Finnish) | 0.00508% | 19,667 |
| Finnishnot grpmax-eligible | 0.00312% | 32,022 |
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
- YTHDF1
- Protein
- p.Lys473=
- Coding
- c.1419G>A
- MANE Select
- NM_017798
- dbSNP
- rs144959355
- Type
- single nucleotide variant
- Location
- chr20:63202521 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI 0.96 (gnomAD)
- Structure
- AlphaFold pLDDT 62.83 · 10 PDB
- Residue 473
- the yth domain; a β-strand
Similar variants
- YTHDF1 p.Asn497= Benign ★★ same type
- YTHDF1 p.His375Tyr 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
- YTHDF1 p.Ala302Gly 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-lys473 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown