YTHDF1 p.Val206=
c.618C>T · VCV3389503
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0294%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9 | GERP -4.3 |
| Overall | ||
| CADD | 0.073 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0294%
African / African-American · 22/74,910 alleles
Filtering AF
0.0199%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0167%
Overall
0.00198%
32/1,613,342 alleles · ultra-rare
exomes 19/1,461,162 · genomes 13/152,180 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0294% | 3,405 |
| East Asian | 0.00445% | 22,447 |
| Admixed American | 0.00167% | 60,008 |
| South Asian | 0.0011% | 91,088 |
| European (non-Finnish) | 0.000508% | 196,660 |
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.Val206=
- Coding
- c.618C>T
- MANE Select
- NM_017798
- Type
- single nucleotide variant
- Location
- chr20:63203322 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI 0.96 (gnomAD)
- Structure
- AlphaFold pLDDT 62.83 · 10 PDB
Similar variants
- YTHDF1 p.Val206Ile Uncertain significance ★ ⚠ same residue
- 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
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-val206 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown