GINS1

GINS complex subunit 1, the group of GINS complex

Basic information

Region (hg38): 20:25391008-25452700

Links

ENSG00000101003NCBI:9837OMIM:610608HGNC:28980Uniprot:Q14691AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Immunodeficiency 55ARAllergy/Immunology/InfectiousThe 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 infectionsAllergy/Immunology/Infectious; Craniofacial; Dermatologic14702466; 28414293

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GINS1 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
26
clinvar
28
missense
2
clinvar
91
clinvar
1
clinvar
94
nonsense
4
clinvar
4
start loss
1
1
frameshift
5
clinvar
5
splice donor/acceptor (+/-2bp)
5
clinvar
5
Total 0 2 108 26 1

Highest pathogenic variant AF is 0.00065956736

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GINS1protein_codingprotein_codingENST00000262460 744902
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
7.70e-70.5021257310161257470.0000636
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2211011070.9400.000005611261
Missense in Polyphen3640.2490.89444434
Synonymous-0.4904137.21.100.00000167363
Loss of Function0.7991114.30.7728.43e-7157

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.0001630.000163
Finnish0.00004700.0000462
European (Non-Finnish)0.00006220.0000615
Middle Eastern0.0001630.000163
South Asian0.0001340.000131
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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