DIDO1 p.Ser537=
c.1611C>T · rs115445869 · VCV769109
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.45%, 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 -5.2 | GERP -2.9 |
| Overall | ||
| CADD | 0.653 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.45%
African / African-American · 2,586/74,898 alleles
Filtering AF
3.34%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.3%
Overall
0.18%
2,898/1,612,910 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.45% | 29 |
| Remaining individualsnot grpmax-eligible | 0.211% | 473 |
| Admixed American | 0.169% | 592 |
| Middle Eastern | 0.0165% | 6,048 |
| European (non-Finnish) | 0.00602% | 16,613 |
| South Asian | 0.00549% | 18,204 |
| East Asian | 0.00223% | 44,886 |
| Finnishnot grpmax-eligible | 0.00157% | 63,750 |
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
- DIDO1
- Protein
- p.Ser537=
- Coding
- c.1611C>T
- MANE Select
- NM_001193369
- dbSNP
- rs115445869
- Type
- single nucleotide variant
- Location
- chr20:62896974 (GRCh38)
- Gene constraint
- LOEUF 0.235 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.89 · 2 PDB
- Residue 537
- the 'disordered' region
Similar variants
- DIDO1 p.Asp1443= Benign ★★ same type
- DIDO1 p.Glu1498Ala Likely benign ★★ same type
- DIDO1 p.Glu1630Lys Benign ★★ same type
- DIDO1 p.Leu1706Val Benign ★★ same type
- DIDO1 p.Pro136= Benign ★★ same type
- DIDO1 p.Pro616Leu Likely benign ★★ same type
- DIDO1 p.Ser877= Benign ★★ same type
- DIDO1 p.Thr1339Ser 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/dido1-p-ser537 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown