MECOM p.Pro201=
c.603G>A · rs1247413105 · VCV2956460
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00668%, 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 -4.4 | GERP -5.6 |
| Overall | ||
| CADD | 8.502 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,888 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000558%
9/1,613,754 alleles · very rare
exomes 7/1,461,652 · genomes 2/152,102 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,963 |
| African / African-American | 0.00134% | 74,880 |
| European (non-Finnish) | 0.000424% | 235,980 |
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
- MECOM
- Protein
- p.Pro201=
- Coding
- c.603G>A
- MANE Select
- NM_004991
- dbSNP
- rs1247413105
- Type
- single nucleotide variant
- Location
- chr3:169131439 (GRCh38)
- Gene constraint
- LOEUF 0.161 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 51.04 · 1 PDB
- Residue 201
- the 'interaction with mapk9, smad3 and probably suv39h1' region
Similar variants
- MECOM p.Pro201Arg Uncertain significance ★ same residue
- MECOM p.Pro201Leu Uncertain significance ★ same residue
- MECOM p.Arg938Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- MECOM p.Arg938Trp Pathogenic/Likely pathogenic ★★ same type
- MECOM p.Thr944Ile Likely pathogenic ★★ same type
- MECOM c.2577+4A>T Uncertain significance ★★ same type
- MECOM c.3585+3A>G Uncertain significance ★★ same type
- MECOM p.Ala1022Gly 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/mecom-p-pro201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown