MMUT p.Pro209=
c.627T>G · rs752307096 · VCV1151159
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00161%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.12 | GERP -2.1, phastCons 0.14 |
| Overall | ||
| CADD | 5.337 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00161%
European (non-Finnish) · 19/1,179,478 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00083%
Overall
0.00118%
19/1,613,420 alleles · very rare
exomes 18/1,461,214 · genomes 1/152,206 · joint denominator
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
- MMUT
- Protein
- p.Pro209=
- Coding
- c.627T>G
- MANE Select
- NM_000255
- dbSNP
- rs752307096
- Type
- single nucleotide variant
- Location
- chr6:49457817 (GRCh38)
- Gene constraint
- LOEUF 1.18 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.72 · 6 PDB
- Residue 209
- a UniProt-annotated variant site (in mamm; mut-); a UniProt-annotated variant site (in mamm; mut0)
Similar variants
- MMUT p.Pro209_Lys210insTer Pathogenic ★★ same residue
- MMUT c.1083+2T>A Pathogenic ★★ same type
- MMUT c.1084-10A>G Pathogenic/Likely pathogenic ★★ same type
- MMUT c.1084-2A>G Pathogenic/Likely pathogenic ★★ same type
- MMUT c.1445-2A>G Pathogenic/Likely pathogenic ★★ same type
- MMUT c.1560+1G>T Pathogenic ★★ same type
- MMUT c.1677-1G>A Pathogenic ★★ same type
- MMUT c.1677-1G>C Pathogenic/Likely pathogenic ★★ 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/mmut-p-pro209 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown