TGOLN2

trans-golgi network protein 2

Basic information

Region (hg38): 2:85318027-85328251

Links

ENSG00000152291 ∙ NCBI:10618 ∙ OMIM:603062 ∙ HGNC:15450 ∙ Uniprot:O43493 ∙ 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 TGOLN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TGOLN2 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						0
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	31	1	0

Variants in TGOLN2

This is a list of pathogenic ClinVar variants found in the TGOLN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-85322694-A-G		not specified	Uncertain significance (Mar 27, 2023)
2-85322748-G-A		not specified	Likely benign (Dec 22, 2023)
2-85326512-C-T		not specified	Uncertain significance (Mar 12, 2024)
2-85326554-G-C		not specified	Uncertain significance (Nov 10, 2021)
2-85326595-G-C		not specified	Uncertain significance (Dec 11, 2023)
2-85326624-G-C		not specified	Uncertain significance (Mar 31, 2024)
2-85326704-T-C		not specified	Uncertain significance (Aug 16, 2022)
2-85326750-C-T		not specified	Uncertain significance (May 03, 2023)
2-85326798-C-A		not specified	Uncertain significance (Jan 23, 2024)
2-85326798-C-T		not specified	Uncertain significance (Nov 01, 2022)
2-85326905-G-C		not specified	Uncertain significance (Jul 20, 2022)
2-85326951-C-T		not specified	Uncertain significance (Jun 29, 2023)
2-85326956-C-G		not specified	Uncertain significance (Jun 05, 2024)
2-85326965-T-G		not specified	Uncertain significance (Mar 27, 2023)
2-85326972-G-C		not specified	Uncertain significance (Sep 17, 2021)
2-85327013-G-C		not specified	Uncertain significance (May 16, 2022)
2-85327016-C-A		not specified	Uncertain significance (Dec 13, 2023)
2-85327077-C-G		not specified	Uncertain significance (May 10, 2022)
2-85327131-G-C		not specified	Uncertain significance (Jan 03, 2024)
2-85327143-C-T		not specified	Uncertain significance (Mar 13, 2023)
2-85327226-C-A		not specified	Uncertain significance (Mar 07, 2023)
2-85327245-C-T		not specified	Uncertain significance (Dec 12, 2023)
2-85327283-C-A		not specified	Uncertain significance (Aug 10, 2023)
2-85327297-C-A		not specified	Uncertain significance (Sep 17, 2021)
2-85327376-G-C		not specified	Uncertain significance (Oct 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TGOLN2	protein_coding	protein_coding	ENST00000409232	4	10402

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00285	0.946	124555	0	8	124563	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.134	239	245	0.976	0.0000133	2930
Missense in Polyphen		80	94.312	0.84824		1060
Synonymous	1.19	86	101	0.850	0.00000650	912
Loss of Function	1.70	6	12.5	0.481	5.49e-7	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000568	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000535	0.0000531
Middle Eastern	0.0000568	0.0000556
South Asian	0.00	0.00
Other	0.000178	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in regulating membrane traffic to and from trans-Golgi network.
• Pathway: Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.183

Intolerance Scores

• loftool: 0.834
• rvis_EVS: 1.42
• rvis_percentile_EVS: 94.89

Haploinsufficiency Scores

• pHI: 0.0599
• hipred: N
• hipred_score: 0.412
• ghis: 0.389

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.265

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tgoln2

Gene ontology

• Biological process: post-translational protein modification;cellular protein metabolic process;membrane organization
• Cellular component: nucleoplasm;endosome;endoplasmic reticulum lumen;Golgi apparatus;trans-Golgi network;plasma membrane;integral component of membrane;transport vesicle;trans-Golgi network transport vesicle;clathrin-coated vesicle membrane
• Molecular function: protein binding