GLMN p.Phe404fs
c.1206_1209del · VCV4541299
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 13 of 19 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.1, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- GLMN
- Protein
- p.Phe404fs
- Coding
- c.1206_1209del
- MANE Select
- NM_053274
- Type
- Deletion
- Location
- chr1:92266424 (GRCh38)
- Gene constraint
- LOEUF 1.705 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 88.41 · 1 PDB
- Residue 404
- the 'alpha-helical region with structural similarity to heat repeats' region; the 'important for interaction with rbx1' region; an α-helix
Similar variants
- GLMN p.Asn393del Pathogenic/Likely pathogenic ★★ same type
- GLMN p.Asn490fs Pathogenic/Likely pathogenic ★★ same type
- GLMN p.Glu196fs Pathogenic/Likely pathogenic ★★ same type
- GLMN p.Glu52_Lys53insTer Pathogenic/Likely pathogenic ★★ same type
- GLMN p.Gly459fs Pathogenic ★★ same type
- GLMN p.Leu282fs Pathogenic/Likely pathogenic ★★ same type
- GLMN p.Leu452fs Pathogenic/Likely pathogenic ★★ same type
- GLMN p.Ser330fs 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/glmn-p-phe404fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown