GLMN p.Asp451=
c.1353T>C · VCV4895720
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, 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 2.7 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 8.795 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,788 alleles
Overall
6.88e-05%
1/1,453,394 alleles · very rare
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.Asp451=
- Coding
- c.1353T>C
- MANE Select
- NM_053274
- Type
- single nucleotide variant
- Location
- chr1:92263679 (GRCh38)
- Gene constraint
- LOEUF 1.705 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 88.41 · 1 PDB
- Residue 451
- the 'alpha-helical region with structural similarity to heat repeats' region; the 'important for interaction with rbx1' region; an α-helix
Similar variants
- GLMN c.1214+2T>C Pathogenic/Likely pathogenic ★★ same type
- GLMN p.Arg574Ter Likely pathogenic ★★ same type
- GLMN p.Cys36Ter Pathogenic/Likely pathogenic ★★ same type
- GLMN p.Ala140Pro Uncertain significance ★★ ⚠ same type
- GLMN p.Ala146Val Uncertain significance ★★ ⚠ same type
- GLMN p.Gln117Glu Uncertain significance ★★ ⚠ same type
- GLMN p.Met168Val Uncertain significance ★★ ⚠ same type
- GLMN p.Ser411Thr 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/glmn-p-asp451 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown