GORASP1

golgi reassembly stacking protein 1, the group of PDZ domain containing

Basic information

Region (hg38): 3:39095222-39108369

Previous symbols: [ "GOLPH5" ]

Links

ENSG00000114745 ∙ NCBI:64689 ∙ OMIM:606867 ∙ HGNC:16769 ∙ Uniprot:Q9BQQ3 ∙ 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 GORASP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GORASP1 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					2	2
missense			28	3	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	28	3	3

Variants in GORASP1

This is a list of pathogenic ClinVar variants found in the GORASP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-39098264-C-T			Benign (Mar 29, 2018)
3-39098265-T-C		not specified	Uncertain significance (Jan 30, 2024)
3-39098287-C-A			Benign (Jan 08, 2018)
3-39098324-T-C		not specified	Uncertain significance (Apr 07, 2022)
3-39098328-C-T		not specified	Uncertain significance (Jan 16, 2025)
3-39098333-G-A		not specified	Uncertain significance (Jul 06, 2021)
3-39098387-CTG-C			Uncertain significance (Feb 21, 2025)
3-39098460-C-T		not specified	Uncertain significance (Jul 30, 2023)
3-39098461-A-C		not specified	Uncertain significance (Jun 23, 2021)
3-39098746-C-T		not specified	Uncertain significance (May 26, 2023)
3-39098747-G-A		not specified	Uncertain significance (Mar 06, 2023)
3-39098806-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-39098863-A-G		not specified	Uncertain significance (Nov 29, 2023)
3-39098878-G-A		not specified	Uncertain significance (Oct 16, 2023)
3-39098882-C-T		not specified	Uncertain significance (Mar 17, 2023)
3-39099365-C-T		not specified	Uncertain significance (Sep 15, 2021)
3-39099401-C-T		not specified	Uncertain significance (Jun 28, 2024)
3-39099427-T-A		not specified	Uncertain significance (Mar 01, 2024)
3-39099437-T-G		not specified	Uncertain significance (Jul 27, 2024)
3-39099451-C-G		not specified	Uncertain significance (Jan 18, 2025)
3-39099490-G-A		not specified	Uncertain significance (Dec 11, 2024)
3-39100337-C-T		not specified	Uncertain significance (Aug 14, 2024)
3-39100355-C-T		not specified	Uncertain significance (Nov 06, 2023)
3-39100373-G-A		not specified	Uncertain significance (Aug 30, 2022)
3-39100402-G-A		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GORASP1	protein_coding	protein_coding	ENST00000319283	9	11705

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0195	0.977	125711	0	36	125747	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.670	216	246	0.880	0.0000132	2824
Missense in Polyphen		67	76.285	0.87829		836
Synonymous	1.42	83	101	0.820	0.00000559	925
Loss of Function	2.55	6	17.5	0.342	8.33e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000360	0.000360
Ashkenazi Jewish	0.00	0.00
East Asian	0.000656	0.000653
Finnish	0.000232	0.000231
European (Non-Finnish)	0.0000712	0.0000703
Middle Eastern	0.000656	0.000653
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in assembly and membrane stacking of the Golgi cisternae, and in the reassembly of Golgi stacks after breakdown during mitosis (PubMed:26363069). Key structural protein required for the maintenance of the Golgi apparatus integrity: its caspase-mediated cleavage is required for fragmentation of the Golgi during apoptosis (By similarity). Also mediates, via its interaction with GOLGA2/GM130, the docking of transport vesicles with the Golgi membranes (PubMed:16489344). {ECO:0000250|UniProtKB:O35254, ECO:0000269|PubMed:16489344, ECO:0000269|PubMed:26363069}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Golgi Cisternae Pericentriolar Stack Reorganization;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Mitotic Prophase;COPI-mediated anterograde transport;M Phase;Cell Cycle;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Cell Cycle, Mitotic;PLK1 signaling events (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: 1.35
• rvis_percentile_EVS: 94.37

Haploinsufficiency Scores

• pHI: 0.282
• hipred: Y
• hipred_score: 0.771
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.943

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gorasp1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein N-linked glycosylation;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;protein transport;COPII vesicle coating;negative regulation of dendrite morphogenesis;establishment of protein localization to plasma membrane;positive regulation of ubiquitin protein ligase activity
• Cellular component: Golgi membrane;Golgi apparatus;endoplasmic reticulum-Golgi intermediate compartment membrane
• Molecular function: protein binding;metal ion binding