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.

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.

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						0
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in GINS3

This is a list of pathogenic ClinVar variants found in the GINS3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-58392623-G-A		not specified	Uncertain significance (Aug 21, 2024)
16-58392626-G-C		not specified	Uncertain significance (Nov 06, 2023)
16-58392641-G-A		not specified	Uncertain significance (Apr 12, 2022)
16-58392666-T-C		not specified	Uncertain significance (Dec 10, 2024)
16-58392674-A-T		not specified	Uncertain significance (Nov 06, 2023)
16-58392719-A-G		not specified	Uncertain significance (Jan 17, 2023)
16-58392750-G-C		not specified	Uncertain significance (Oct 02, 2023)
16-58392761-G-T		not specified	Uncertain significance (Jan 03, 2025)
16-58395172-C-A		GINS3-related disorder	Likely benign (Apr 25, 2023)
16-58403137-C-G		not specified	Uncertain significance (Mar 11, 2022)
16-58403153-G-A		not specified	Uncertain significance (May 13, 2019)
16-58403155-C-T		not specified	Uncertain significance (Oct 17, 2024)
16-58403156-G-A		not specified	Uncertain significance (Jun 03, 2022)
16-58403173-C-A		not specified	Uncertain significance (Aug 11, 2022)
16-58403198-G-C		not specified	Uncertain significance (Oct 05, 2017)
16-58403224-A-T		not specified	Uncertain significance (Feb 13, 2025)
16-58403290-G-A		not specified	Uncertain significance (Oct 06, 2022)
16-58403291-A-G		not specified	Uncertain significance (Jul 19, 2023)
16-58404511-C-T		not specified	Uncertain significance (Apr 09, 2024)
16-58404517-C-T		not specified	Uncertain significance (Jan 16, 2025)
16-58404521-G-T		not specified	Uncertain significance (Apr 01, 2024)
16-58404533-C-A		not specified	Uncertain significance (Dec 15, 2024)
16-58404553-G-A		not specified	Uncertain significance (Jan 26, 2025)
16-58404637-C-G		not specified	Uncertain significance (Mar 14, 2025)
16-58404719-T-C		not specified	Uncertain significance (May 30, 2023)

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

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