GINS2
Basic information
Region (hg38): 16:85676198-85690073
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (52 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GINS2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016095.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 52 | 52 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 52 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GINS2 | protein_coding | protein_coding | ENST00000253462 | 5 | 13876 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.57e-8 | 0.0657 | 125708 | 0 | 40 | 125748 | 0.000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.32 | 138 | 101 | 1.37 | 0.00000560 | 1209 |
| Missense in Polyphen | 41 | 35.944 | 1.1407 | 403 | ||
| Synonymous | -3.26 | 62 | 36.9 | 1.68 | 0.00000206 | 332 |
| Loss of Function | -0.518 | 11 | 9.30 | 1.18 | 5.79e-7 | 103 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000307 | 0.000304 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000393 | 0.000381 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.000217 | 0.000202 |
| Middle Eastern | 0.000393 | 0.000381 |
| South Asian | 0.0000658 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: The GINS complex plays an essential role in the initiation of DNA replication, and progression of DNA replication forks. GINS complex seems to bind preferentially to single- stranded DNA. {ECO:0000269|PubMed:17417653}.;
- Pathway
- Unwinding of DNA;DNA Replication;DNA strand elongation;Synthesis of DNA;S Phase;Cell Cycle;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- 0.451
- rvis_EVS
- -0.74
- rvis_percentile_EVS
- 13.94
Haploinsufficiency Scores
- pHI
- 0.571
- hipred
- Y
- hipred_score
- 0.779
- ghis
- 0.727
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.802
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gins2
- Phenotype
Gene ontology
- Biological process
- double-strand break repair via break-induced replication;DNA strand elongation involved in DNA replication;DNA duplex unwinding
- Cellular component
- GINS complex;nucleoplasm;replication fork protection complex
- Molecular function
- protein binding;3'-5' DNA helicase activity