YTHDF1 p.Ser341=
c.1023C>T · rs769739642 · VCV2652517
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00445%, eas)
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 -1.8 | GERP -4.3 |
| Overall | ||
| CADD | 0.361 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00445%
East Asian · 2/44,896 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.0013%
21/1,613,904 alleles · very rare
exomes 16/1,461,674 · genomes 5/152,230 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00445% | 22,448 |
| African / African-American | 0.004% | 24,983 |
| Finnishnot grpmax-eligible | 0.00313% | 31,909 |
| South Asian | 0.0022% | 45,546 |
| European (non-Finnish) | 0.00102% | 98,338 |
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.Ser341=
- Coding
- c.1023C>T
- MANE Select
- NM_017798
- dbSNP
- rs769739642
- Type
- single nucleotide variant
- Location
- chr20:63202917 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI 0.96 (gnomAD)
- Structure
- AlphaFold pLDDT 62.83 · 10 PDB
- Residue 341
- the 'disordered' region
Similar variants
- YTHDF1 p.Ser341Asn 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-ser341 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown