MGP p.Leu7Pro
c.20T>C · VCV4726047
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely benign
0.1516 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/2 damaging
AlphaMissense, SaProt · REVEL indeterminate
Computational evidence
| Protein change | ||
| AlphaMissense | 0.1516 | likely benign |
|---|---|---|
| REVEL | 0.354 | indeterminate |
| SaProt | LLR -14.35 | damaging |
| ⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 9.2 | GERP 1.9, phastCons 1 |
| Regional constraint | o/e 0.96 | unconstrained · MANE · 3,649 bp · p 0.62 · regional, not allelic |
| Overall | ||
| CADD | 23.5 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- MGP
- Protein
- p.Leu7Pro
- Coding
- c.20T>C
- MANE Select
- NM_000900
- Type
- single nucleotide variant
- Location
- chr12:14885772 (GRCh38)
- Gene constraint
- LOEUF 1.63 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 82.56 · 3 PDB
Similar variants
- MGP c.94+1G>A Pathogenic/Likely pathogenic ★★ same type
- MGP c.94+5G>A Uncertain significance ★★ same type
- MGP p.Arg61His Uncertain significance ★★ ⚠ same type
- MGP p.Gln47Glu Uncertain significance ★★ ⚠ same type
- MGP p.Met26Thr Uncertain significance ★★ ⚠ same type
- MGP p.Tyr76His Uncertain significance ★★ ⚠ same type
- MGP c.171-67T>A Likely benign ★★ same type
- MGP c.61+10T>G Likely 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/mgp-p-leu7pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown