GINS2

GINS complex subunit 2, the group of GINS complex

Basic information

Region (hg38): 16:85676198-85690073

Links

ENSG00000131153 ∙ NCBI:51659 ∙ OMIM:610609 ∙ HGNC:24575 ∙ Uniprot:Q9Y248 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GINS2 gene.

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.

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			35			35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	35	0	1

Variants in GINS2

This is a list of pathogenic ClinVar variants found in the GINS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-85678238-C-G		not specified	Uncertain significance (Sep 12, 2023)
16-85678241-G-C		not specified	Uncertain significance (Apr 17, 2024)
16-85678244-G-C		not specified	Uncertain significance (Jun 06, 2023)
16-85678250-G-T		not specified	Uncertain significance (Jul 03, 2024)
16-85678253-T-A		not specified	Uncertain significance (Mar 15, 2024)
16-85678258-C-T		not specified	Uncertain significance (Jul 26, 2022)
16-85678259-G-A		not specified	Uncertain significance (Sep 01, 2021)
16-85678274-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-85678294-A-C		not specified	Uncertain significance (May 30, 2022)
16-85678301-C-T		not specified	Uncertain significance (Jun 26, 2024)
16-85678309-T-G		not specified	Uncertain significance (Jun 30, 2022)
16-85678324-G-A		not specified	Uncertain significance (Jul 08, 2021)
16-85678333-T-C		not specified	Uncertain significance (Jan 03, 2024)
16-85678531-G-A			Benign (Jul 13, 2018)
16-85678544-G-C		not specified	Uncertain significance (Dec 08, 2023)
16-85678573-G-C		not specified	Uncertain significance (Feb 28, 2024)
16-85678584-C-T		not specified	Uncertain significance (Apr 24, 2024)
16-85678601-C-A		not specified	Uncertain significance (Sep 26, 2023)
16-85678604-G-A		not specified	Uncertain significance (Dec 27, 2022)
16-85678608-C-G		not specified	Uncertain significance (Aug 28, 2023)
16-85678612-C-A		not specified	Uncertain significance (Sep 26, 2022)
16-85678618-C-A		not specified	Uncertain significance (May 30, 2023)
16-85678626-G-C		not specified	Uncertain significance (Oct 20, 2024)
16-85678638-C-T		not specified	Uncertain significance (Jul 02, 2024)
16-85678649-G-A		not specified	Uncertain significance (Nov 11, 2024)

GnomAD

Source: gnomAD

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: 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)

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

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