MYB p.Ser405Pro
c.1213T>C · rs73555742 · VCV785188
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 4.07%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.029 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.11 | GERP -1.5, phastCons 0.99 |
| Regional constraint | o/e 0.93 | unconstrained · MANE · 22 kb · p 0.12 · regional, not allelic |
| Overall | ||
| CADD | 19.94 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.07%
African / African-American · 3,056/75,018 alleles
Filtering AF
3.95%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.9%
Overall
0.214%
3,445/1,612,764 alleles · low-frequency
exomes 1,648/1,460,440 · genomes 1,797/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.07% | 25 |
| Admixed American | 0.304% | 329 |
| Remaining individualsnot grpmax-eligible | 0.231% | 434 |
| Middle Eastern | 0.066% | 1,515 |
| European (non-Finnish) | 0.00492% | 20,334 |
| South Asian | 0.0011% | 90,924 |
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
- MYB
- Protein
- p.Ser405Pro
- Coding
- c.1213T>C
- MANE Select
- NM_001130173
- dbSNP
- rs73555742
- Type
- single nucleotide variant
- Location
- chr6:135196970 (GRCh38)
- Gene constraint
- LOEUF 0.443 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 59.16
- Residue 405
- the 'negative regulatory domain' region
Similar variants
- MYB p.Thr589= Benign/Likely benign ★★ same type
- MYB p.Ala278Thr Uncertain significance ★ ⚠ same type
- MYB p.Ala470Ser Uncertain significance ★ same type
- MYB p.Ala491Asp Uncertain significance ★ same type
- MYB p.Ala719Glu Uncertain significance ★ ⚠ same type
- MYB p.Arg337Gly Uncertain significance ★ ⚠ same type
- MYB p.Arg484Trp Uncertain significance ★ same type
- MYB p.Arg4Ser 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/myb-p-ser405pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown