GORASP2

golgi reassembly stacking protein 2, the group of PDZ domain containing

Basic information

Region (hg38): 2:170928463-170967130

Links

ENSG00000115806 ∙ NCBI:26003 ∙ OMIM:608693 ∙ HGNC:17500 ∙ Uniprot:Q9H8Y8 ∙ 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 GORASP2 gene.

• Inborn genetic diseases (22 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GORASP2 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
missense			21	1	1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	2

Variants in GORASP2

This is a list of pathogenic ClinVar variants found in the GORASP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-170948390-C-T		not specified	Uncertain significance (Jun 27, 2022)
2-170949581-G-A		not specified	Uncertain significance (Jan 24, 2024)
2-170949633-G-A		not specified	Uncertain significance (Jun 29, 2023)
2-170949644-G-A		not specified	Uncertain significance (Feb 16, 2023)
2-170949720-A-G		not specified	Uncertain significance (Mar 06, 2023)
2-170951346-C-T		not specified	Uncertain significance (Nov 22, 2021)
2-170954696-C-T		not specified	Uncertain significance (Aug 17, 2022)
2-170954723-T-C		not specified	Uncertain significance (Mar 01, 2023)
2-170954750-C-T		not specified	Uncertain significance (May 30, 2023)
2-170956457-C-G		not specified	Uncertain significance (Aug 04, 2021)
2-170956488-G-A		not specified	Likely benign (May 27, 2022)
2-170961682-A-C		not specified	Uncertain significance (Jan 19, 2024)
2-170961692-C-G		not specified	Uncertain significance (Nov 08, 2022)
2-170961714-C-T		not specified	Uncertain significance (May 22, 2023)
2-170961734-G-C		not specified	Uncertain significance (Feb 10, 2022)
2-170965840-C-T		not specified	Uncertain significance (Apr 12, 2022)
2-170965849-C-T			Benign (May 21, 2018)
2-170965852-C-A		not specified	Uncertain significance (Oct 17, 2023)
2-170965877-C-T		not specified	Uncertain significance (Jan 13, 2023)
2-170965895-C-G		not specified	Uncertain significance (Mar 01, 2024)
2-170965948-G-A		not specified	Uncertain significance (Jul 16, 2021)
2-170965957-G-C		not specified	Uncertain significance (Dec 20, 2023)
2-170965969-A-G		not specified	Uncertain significance (Aug 02, 2021)
2-170966009-A-C		not specified	Uncertain significance (Jun 07, 2023)
2-170966015-C-T			Benign (Apr 17, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GORASP2	protein_coding	protein_coding	ENST00000234160	10	38666

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.884	0.116	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	175	245	0.714	0.0000124	2865
Missense in Polyphen		23	44.994	0.51118		534
Synonymous	0.438	92	97.5	0.944	0.00000551	980
Loss of Function	3.55	3	20.2	0.148	0.00000116	236

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the assembly and membrane stacking of the Golgi cisternae, and in the process by which Golgi stacks reform after breakdown during mitosis and meiosis (PubMed:10487747, PubMed:21515684, PubMed:22523075). May regulate the intracellular transport and presentation of a defined set of transmembrane proteins, such as transmembrane TGFA (PubMed:11101516). Required for normal acrosome formation during spermiogenesis and normal male fertility, probably by promoting colocalization of JAM2 and JAM3 at contact sites between germ cells and Sertoli cells (By similarity). {ECO:0000250|UniProtKB:Q99JX3, ECO:0000269|PubMed:10487747, ECO:0000269|PubMed:11101516, ECO:0000269|PubMed:21515684, ECO:0000269|PubMed:22523075}.
• Pathway: Golgi Cisternae Pericentriolar Stack Reorganization;Mitotic Prophase;M Phase;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.148

Intolerance Scores

• loftool: 0.455
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.306
• hipred: Y
• hipred_score: 0.696
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.817

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gorasp2
• Phenotype: reproductive system phenotype; growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: organelle organization;Golgi organization;spermatogenesis;cell differentiation;response to endoplasmic reticulum stress;establishment of protein localization to plasma membrane;organelle assembly
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;Golgi apparatus;membrane
• Molecular function: protein binding