Is GLMN p.Ser360fs (c.1078_1079del) pathogenic?

GLMN p.Ser360fs (c.10781079del) is classified Pathogenic in GLMN (ClinVar, Single submitter, 1 submitter; last evaluated 2020-04-10). Absent from gnomAD.

How common is GLMN p.Ser360fs (c.1078_1079del) in the general population?

GLMN p.Ser360fs (c.1078_1079del) is absent from gnomAD (gnomAD).

GLMN p.Ser360fs

c.1078_1079del · rs2100903095 · VCV1073647

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 11 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3	GERP 0.96, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

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.Ser360fs
Coding: c.1078_1079del
MANE Select: NM_053274
dbSNP: rs2100903095
Type: Microsatellite
Location: chr1:92267932 (GRCh38)
Gene constraint: LOEUF 1.705 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 88.41 · 1 PDB
Residue 360: the 'alpha-helical region with structural similarity to heat repeats' region; the 'important for interaction with rbx1' region; an α-helix

Full GLMN gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GLMN p.Ser384fs Pathogenic/Likely pathogenic ★★ same type
GLMN c.1410-19AT[2] Likely benign ★★ same type
GLMN c.980_984del Likely pathogenic ★ same type
GLMN p.Arg12fs Pathogenic ★ same type
GLMN p.Asp566_Leu567insTer Uncertain significance ★ same type
GLMN c.1410-24_1410-21del 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/glmn-p-ser360fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown