YEATS2 p.Ser481=
c.1443C>T · rs201314461 · VCV712703
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.256%, nfe)
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 0.5 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 8.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.256%
European (non-Finnish) · 3,012/1,176,766 alleles
Filtering AF
0.248%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.245%
Overall
0.201%
3,227/1,606,838 alleles · rare
exomes 3,030/1,454,552 · genomes 197/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.256% | 391 |
| Remaining individualsnot grpmax-eligible | 0.128% | 778 |
| Admixed American | 0.12% | 831 |
| Finnishnot grpmax-eligible | 0.0578% | 1,730 |
| African / African-American | 0.032% | 3,121 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,564 |
| South Asian | 0.00225% | 44,393 |
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
- YEATS2
- Protein
- p.Ser481=
- Coding
- c.1443C>T
- MANE Select
- NM_018023
- dbSNP
- rs201314461
- Type
- single nucleotide variant
- Location
- chr3:183756580 (GRCh38)
- Gene constraint
- LOEUF 0.552 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 51.50 · 5 PDB
- Residue 481
- the 'disordered' region
Similar variants
- YEATS2 p.Ser481Phe Uncertain significance ★ ⚠ same residue
- YEATS2 p.Asp12Asn Uncertain significance ★★ ⚠ same type
- YEATS2 p.His1216Arg Uncertain significance ★★ ⚠ same type
- YEATS2 c.292-27T>C Benign/Likely benign ★★ same type
- YEATS2 c.3582+10A>G Benign ★★ same type
- YEATS2 p.Ala1000Thr Benign/Likely benign ★★ same type
- YEATS2 p.Ala603Thr Likely benign ★★ same type
- YEATS2 p.Ile495Met Likely benign ★★ 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/yeats2-p-ser481 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown