Is GLMN p.Ser384fs (c.1150_1151del) pathogenic?

GLMN p.Ser384fs (c.11501151del) is classified Pathogenic/Likely pathogenic in GLMN (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-04-06). Very rare (popmax 0.00271%, afr); Associated with GLMN-related disorders.

What condition is associated with GLMN p.Ser384fs (c.1150_1151del)?

GLMN p.Ser384fs (c.1150_1151del) is associated with GLMN-related disorders, glomuvenous malformation (ClinVar).

How common is GLMN p.Ser384fs (c.1150_1151del) in the general population?

GLMN p.Ser384fs (c.1150_1151del) is very rare (popmax 0.00271%, afr) (gnomAD).

GLMN p.Ser384fs

c.1150_1151del · rs750074519 · VCV1691366

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00271%, afr)

Conditions

GLMN-related disorders

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 0.34	GERP -4.1, phastCons 0.13
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00271% African / African-American · 2/73,840 alleles

Filtering AF 0.00045% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000168%

Overall 0.00064% 10/1,563,532 alleles · very rare exomes 9/1,411,412 · genomes 1/152,120 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00271%	36,920
East Asian	0.00225%	44,514
Admixed American	0.00168%	59,692
Remaining individualsnot grpmax-eligible	0.00165%	60,664
European (non-Finnish)	0.00044%	227,111

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.Ser384fs
Coding: c.1150_1151del
MANE Select: NM_053274
dbSNP: rs750074519
Type: Microsatellite
Location: chr1:92266482 (GRCh38)
Gene constraint: LOEUF 1.705 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 88.41 · 1 PDB
Residue 384: 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

Disease context

GLMN-related disorders

Also linked: glomuvenous malformation

Similar variants

GLMN c.1410-19AT[2] Likely benign ★★ same condition
GLMN c.980_984del Likely pathogenic ★ same condition
GLMN p.Arg12fs Pathogenic ★ same condition
GLMN p.Arg574Ter Likely pathogenic ★★ same condition
GLMN p.Asn393del Pathogenic/Likely pathogenic ★★ same condition
GLMN p.Asn490fs Pathogenic/Likely pathogenic ★★ same condition
GLMN p.Cys36Ter Pathogenic/Likely pathogenic ★★ same condition
GLMN p.Glu196fs Pathogenic/Likely pathogenic ★★ 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-ser384fs (accessed [today's date]).

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