GINS1
Basic information
Region (hg38): 20:25391008-25452700
Links
Phenotypes
GenCC
Source:
- combined immunodeficiency due to GINS1 deficiency (Supportive), mode of inheritance: AR
- combined immunodeficiency due to GINS1 deficiency (Limited), mode of inheritance: Unknown
- combined immunodeficiency due to GINS1 deficiency (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Immunodeficiency 55 | AR | Allergy/Immunology/Infectious | The condition can include early-onset, severe, and recurrent infections, as well as other immunologic sequelae, and awareness may allow antiinfectious prophylaxis and early and aggressive treatment of infections | Allergy/Immunology/Infectious; Craniofacial; Dermatologic | 14702466; 28414293 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (158 variants)
- not_specified (25 variants)
- Combined_immunodeficiency_due_to_GINS1_deficiency (5 variants)
- GINS1-related_disorder (4 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GINS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021067.5. 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 | 26 | 28 | ||||
missense | 91 | 94 | ||||
nonsense | 4 | |||||
start loss | 1 | 1 | ||||
frameshift | 5 | |||||
splice donor/acceptor (+/-2bp) | 5 | |||||
Total | 0 | 2 | 108 | 26 | 1 |
Highest pathogenic variant AF is 0.00065956736
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GINS1 | protein_coding | protein_coding | ENST00000262460 | 7 | 44902 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
7.70e-7 | 0.502 | 125731 | 0 | 16 | 125747 | 0.0000636 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.221 | 101 | 107 | 0.940 | 0.00000561 | 1261 |
Missense in Polyphen | 36 | 40.249 | 0.89444 | 434 | ||
Synonymous | -0.490 | 41 | 37.2 | 1.10 | 0.00000167 | 363 |
Loss of Function | 0.799 | 11 | 14.3 | 0.772 | 8.43e-7 | 157 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000289 | 0.0000289 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.0000470 | 0.0000462 |
European (Non-Finnish) | 0.0000622 | 0.0000615 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.000134 | 0.000131 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for correct functioning of the GINS complex, a complex that 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, ECO:0000269|PubMed:28414293}.;
- Disease
- DISEASE: Immunodeficiency 55 (IMD55) [MIM:617827]: An autosomal recessive primary immunodeficiency characterized by chronic neutropenia, natural killer cell deficiency, recurrent viral and bacterial infections, and intrauterine growth retardation. Postnatal growth retardation is present in most patients. {ECO:0000269|PubMed:28414293}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Unwinding of DNA;DNA Replication;DNA strand elongation;Synthesis of DNA;S Phase;Cell Cycle;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.147
Intolerance Scores
- loftool
- 0.598
- rvis_EVS
- 0.3
- rvis_percentile_EVS
- 72.01
Haploinsufficiency Scores
- pHI
- 0.0920
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.632
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.438
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gins1
- Phenotype
- embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cellular phenotype;
Gene ontology
- Biological process
- inner cell mass cell proliferation;DNA strand elongation involved in DNA replication;DNA duplex unwinding;DNA strand elongation involved in mitotic DNA replication
- Cellular component
- GINS complex;nucleus;nucleoplasm;cytoplasm
- Molecular function
- 3'-5' DNA helicase activity