MYMK p.Pro205=
c.615G>A · rs146986769 · VCV742255
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.03%, eas)
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 -20 | GERP -2.4 |
| Overall | ||
| CADD | 0.067 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.03%
East Asian · 460/44,866 alleles
Filtering AF
0.948%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.917%
Overall
0.031%
500/1,613,982 alleles · low-frequency
exomes 448/1,461,694 · genomes 52/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.03% | 98 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,208 |
| Middle Eastern | 0.0165% | 6,060 |
| African / African-American | 0.0107% | 9,381 |
| South Asian | 0.00878% | 11,386 |
| Admixed American | 0.005% | 20,004 |
| European (non-Finnish) | 0.000678% | 147,485 |
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
- MYMK
- Protein
- p.Pro205=
- Coding
- c.615G>A
- MANE Select
- NM_001080483
- dbSNP
- rs146986769
- Type
- single nucleotide variant
- Location
- chr9:133514687 (GRCh38)
- Gene constraint
- LOEUF 1.02 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.14
Similar variants
- MYMK p.Pro205Leu Uncertain significance ★ ⚠ same residue
- MYMK p.Gly100Ser Pathogenic/Likely pathogenic ★★ same type
- MYMK p.Pro91Thr Pathogenic/Likely pathogenic ★★ same type
- MYMK c.399+5G>A Uncertain significance ★★ same type
- MYMK p.Asp64Asn Uncertain significance ★★ ⚠ same type
- MYMK p.Leu143Pro Uncertain significance ★★ ⚠ same type
- MYMK c.135+81T>G Benign ★★ same type
- MYMK c.136-27T>C 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/mymk-p-pro205 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown