GLG1

golgi glycoprotein 1

Basic information

Region (hg38): 16:74447427-74607144

Links

ENSG00000090863 ∙ NCBI:2734 ∙ OMIM:600753 ∙ HGNC:4316 ∙ Uniprot:Q92896 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GLG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLG1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			59			59
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	59	2	1

Variants in GLG1

This is a list of pathogenic ClinVar variants found in the GLG1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-74452111-G-T		not specified	Uncertain significance (Jul 12, 2023)
16-74452126-T-G		not specified	Uncertain significance (Nov 30, 2021)
16-74452127-G-A			Likely benign (Oct 10, 2018)
16-74453200-G-A			Likely benign (Jun 01, 2022)
16-74453272-G-C		not specified	Uncertain significance (Aug 30, 2021)
16-74456690-G-A		not specified	Uncertain significance (Mar 07, 2023)
16-74457876-C-T		not specified	Uncertain significance (Nov 10, 2022)
16-74457901-C-T		not specified	Uncertain significance (Oct 04, 2022)
16-74459691-C-A		not specified	Uncertain significance (May 18, 2023)
16-74459783-T-C		not specified	Uncertain significance (Apr 20, 2023)
16-74462164-C-T		not specified	Uncertain significance (Oct 26, 2021)
16-74462520-T-C		not specified	Uncertain significance (May 10, 2024)
16-74462533-T-G		not specified	Uncertain significance (May 04, 2022)
16-74462582-G-A		not specified	Uncertain significance (Apr 28, 2022)
16-74462611-C-T		not specified	Uncertain significance (Jul 31, 2023)
16-74463372-C-G		not specified	Uncertain significance (Jul 12, 2023)
16-74463373-T-A		not specified	Uncertain significance (Jul 12, 2023)
16-74463386-T-C		not specified	Uncertain significance (Dec 14, 2023)
16-74463442-T-C		not specified	Uncertain significance (Jun 21, 2023)
16-74465771-G-C		not specified	Uncertain significance (Oct 26, 2021)
16-74468965-C-T		not specified	Uncertain significance (Jun 06, 2023)
16-74469025-T-C		not specified	Uncertain significance (Jun 10, 2024)
16-74469037-G-A		not specified	Uncertain significance (May 27, 2022)
16-74470038-A-T		not specified	Uncertain significance (Jan 16, 2024)
16-74470054-C-T		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLG1	protein_coding	protein_coding	ENST00000205061	27	155157

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000222	125418	0	329	125747	0.00131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.07	546	700	0.780	0.0000395	7926
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00487	0.00470
Ashkenazi Jewish	0.000499	0.000496
East Asian	0.00302	0.00299
Finnish	0.00393	0.00389
European (Non-Finnish)	0.000887	0.000879
Middle Eastern	0.00302	0.00299
South Asian	0.0000328	0.0000327
Other	0.000498	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds fibroblast growth factor and E-selectin (cell- adhesion lectin on endothelial cells mediating the binding of neutrophils).
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Cell surface interactions at the vascular wall;Hemostasis;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.159

Intolerance Scores

• loftool: 0.0109
• rvis_EVS: -1.68
• rvis_percentile_EVS: 2.65

Haploinsufficiency Scores

• pHI: 0.180
• hipred: Y
• hipred_score: 0.538
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.696

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glg1
• Phenotype: growth/size/body region phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; skeleton phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; limbs/digits/tail phenotype; immune system phenotype

Gene ontology

• 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
• Cellular component: Golgi membrane;Golgi apparatus;plasma membrane;membrane;integral component of membrane;extracellular matrix;extracellular exosome
• Molecular function: signaling receptor binding;fibroblast growth factor binding