GLMN p.Glu545=
c.1635G>A · rs376960198 · VCV298127
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0332%, mid)
Conditions
1
glomuvenous malformation
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 -0.48 | GERP -0.7, phastCons 0.031 |
| Overall | ||
| CADD | 5.509 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0332%
Middle Eastern · 2/6,018 alleles
Filtering AF
0.009%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00682%
Overall
0.00393%
62/1,577,988 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0332% | 3,009 |
| Admixed American | 0.0167% | 5,995 |
| Finnishnot grpmax-eligible | 0.0111% | 8,996 |
| Remaining individualsnot grpmax-eligible | 0.00816% | 12,262 |
| European (non-Finnish) | 0.00331% | 30,214 |
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
- GLMN
- Protein
- p.Glu545=
- Coding
- c.1635G>A
- MANE Select
- NM_053274
- dbSNP
- rs376960198
- Type
- single nucleotide variant
- Location
- chr1:92247095 (GRCh38)
- Gene constraint
- LOEUF 1.705 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 88.41 · 1 PDB
- Residue 545
- the 'alpha-helical region with structural similarity to heat repeats' region; the 'important for interaction with rbx1' region
Similar variants
- GLMN p.Cys36Ter Pathogenic/Likely pathogenic ★★ same condition
- GLMN p.Ala140Pro Uncertain significance ★★ ⚠ same condition
- GLMN p.Ala146Val Uncertain significance ★★ ⚠ same condition
- GLMN p.Ser411Thr Uncertain significance ★★ ⚠ same condition
- GLMN p.Val191Phe Uncertain significance ★★ ⚠ same condition
- GLMN c.165+10A>G Benign/Likely benign ★★ same condition
- GLMN c.977+7T>A Benign ★★ same condition
- GLMN c.977+9G>A Benign ★★ same condition
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/glmn-p-glu545 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown