GINS3

GINS complex subunit 3, the group of GINS complex

Basic information

Region (hg38): 16:58295080-58406147

Links

ENSG00000181938

∙ NCBI:64785 ∙ OMIM:610610 ∙ HGNC:25851 ∙ Uniprot:Q9BRX5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Meier-Gorlin syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GINS3 gene.

not_specified (35 variants)
GINS3-related_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GINS3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022770.4. 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			35 clinvar			35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	35	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GINS3	protein_coding	protein_coding	ENST00000426538	4	111065

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000150	0.428	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.459	118	133	0.888	0.00000692	1660
Missense in Polyphen		24	32.826	0.73113		394
Synonymous	-0.435	58	53.9	1.08	0.00000289	514
Loss of Function	0.424	8	9.40	0.851	4.89e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000308	0.000308
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.000324	0.000323
European (Non-Finnish)	0.0000885	0.0000879
Middle Eastern	0.000219	0.000217
South Asian	0.000165	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

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)

Intolerance Scores

loftool: 0.227
rvis_EVS: -0.12
rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

pHI: 0.239
hipred: Y
hipred_score: 0.723
ghis: 0.626

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: N
gene_indispensability_score: 0.373

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Gins3
Phenotype

Zebrafish Information Network

Gene name: gins3
Affected structure: head
Phenotype tag: abnormal
Phenotype quality: decreased width

Gene ontology

Biological process: DNA strand elongation involved in DNA replication
Cellular component: nucleoplasm
Molecular function: protein binding