GLMN p.Phe563fs
c.1687_1688del · rs2523729338 · VCV2672089
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 | escapes | premature termination codon in the last exon (19 of 19) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 6.7 | GERP 0.19, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- GLMN
- Protein
- p.Phe563fs
- Coding
- c.1687_1688del
- MANE Select
- NM_053274
- dbSNP
- rs2523729338
- Type
- Deletion
- Location
- chr1:92246627 (GRCh38)
- Gene constraint
- LOEUF 1.705 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 88.41 · 1 PDB
- Residue 563
- the 'important for interaction with rbx1' region; an α-helix
Similar variants
- GLMN p.Asn393del Pathogenic/Likely pathogenic ★★ same condition
- GLMN p.Glu196fs Pathogenic/Likely pathogenic ★★ same condition
- GLMN p.Glu52_Lys53insTer Pathogenic/Likely pathogenic ★★ same condition
- GLMN p.Gly459fs Pathogenic ★★ same condition
- GLMN p.Leu282fs Pathogenic/Likely pathogenic ★★ same condition
- GLMN p.Leu452fs Pathogenic/Likely pathogenic ★★ same condition
- GLMN p.Ser330fs Pathogenic/Likely pathogenic ★★ same condition
- GLMN c.40-6del 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-phe563fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown