GORASP2
Basic information
Region (hg38): 2:170928464-170967130
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 38 | 40 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 38 | 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 |
---|---|---|---|---|
2-170929395-G-A | not specified | Uncertain significance (Jul 27, 2024) | ||
2-170948390-C-T | not specified | Uncertain significance (Jun 27, 2022) | ||
2-170949581-G-A | not specified | Uncertain significance (Jan 24, 2024) | ||
2-170949607-C-G | not specified | Uncertain significance (Oct 06, 2024) | ||
2-170949627-A-C | not specified | Uncertain significance (Nov 14, 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) | ||
2-170951352-G-A | not specified | Uncertain significance (Jul 26, 2024) | ||
2-170954696-C-T | not specified | Uncertain significance (Aug 17, 2022) | ||
2-170954723-T-C | not specified | Uncertain significance (Mar 01, 2023) | ||
2-170954726-C-T | not specified | Uncertain significance (Aug 01, 2024) | ||
2-170954750-C-T | not specified | Uncertain significance (May 30, 2023) | ||
2-170956436-G-T | not specified | Uncertain significance (Oct 19, 2024) | ||
2-170956457-C-G | not specified | Uncertain significance (Aug 04, 2021) | ||
2-170956485-C-T | not specified | Uncertain significance (Aug 05, 2024) | ||
2-170956488-G-A | not specified | Likely benign (May 27, 2022) | ||
2-170956555-T-G | not specified | Uncertain significance (Aug 01, 2024) | ||
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) |
GnomAD
Source:
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:
- 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