GLG1

protein-coding

golgi glycoprotein 1

Gene summary

Predicted to enable fibroblast growth factor binding activity. Predicted to act upstream of or within several processes, including negative regulation of protein processing; negative regulation of transforming growth factor beta receptor signaling pathway; and regulation of chondrocyte differentiation. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001145667.2

Inheritance

—

ClinVar variants

U:148B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr16:74,447,427-74,607,144

External References & Databases

Ensembl (ENSG00000090863)

Transcript & Mutation Effects

hg38 • Region Span ~159.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GLG1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 131

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001145667.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			136 clinvar			136
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	148	1	0	149

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001145667.2	RefSeq	NP_001139139.1	26	MANE Select
ENST00000422840.7	Ensembl	ENSP00000405984.3	26	MANE Select
NM_001145666.2	RefSeq	NP_001139138.1	26	Standard
NM_012201.6	RefSeq	NP_036333.2	27	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cell adhesion molecules (CAMs) - Homo sapiens (human)
Cell surface interactions at the vascular wall
Hemostasis
TNFalpha

Biological Process

negative regulation of protein processing
negative regulation of transforming growth factor beta receptor signaling pathway
regulation of chondrocyte differentiation
leukocyte migration
bone morphogenesis

Molecular Function

signaling receptor binding
fibroblast growth factor binding

Cellular Component

Golgi membrane
Golgi apparatus
plasma membrane
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000205061
Coding exons: 27
Length: 155157
Individuals with no LoFs: 125418
Homozygous LoFs: 0
Heterozygous LoFs: 329
Defined: 125747
p: 0.00131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.07	546	700	0.780	0.0000395	7926
Missense (PolyPhen)		61	181.82	0.33549		2051
Synonymous	-3.53	329	257	1.28	0.0000139	2204
Loss of Function	7.12	9	76.0	0.118	0.00000445	819

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0046	0.0044	notable
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.0030	0.0030	notable
Finnish	0.0039	0.0039	notable
European (Non-Finnish)	0.00089	0.00088	rare
South Asian	0.000033	0.000033	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds fibroblast growth factor and E-selectin (cell- adhesion lectin on endothelial cells mediating the binding of neutrophils).;

Recessive Scores

pRec: 0.159

Intolerance Scores

LoFtool: 0.0109
RVIS EVS: -1.68
RVIS percentile EVS: 2.65

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.696

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium