MGP p.Lys98=
c.294G>A · rs527610060 · VCV1624298
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0627%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.022 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.97 | GERP 0.2, phastCons 1 |
| Overall | ||
| CADD | 6.71 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0627%
African / African-American · 47/75,018 alleles
Filtering AF
0.0483%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0433%
Overall
0.00322%
52/1,614,062 alleles · ultra-rare
exomes 25/1,461,812 · genomes 27/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0627% | 1,596 |
| Admixed American | 0.005% | 20,004 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,252 |
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
- MGP
- Protein
- p.Lys98=
- Coding
- c.294G>A
- MANE Select
- NM_000900
- dbSNP
- rs527610060
- Type
- single nucleotide variant
- Location
- chr12:14882157 (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-lys98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown