GINS4

GINS complex subunit 4, the group of GINS complex

Basic information

Region (hg38): 8:41529217-41545030

Links

ENSG00000147536 ∙ NCBI:84296 ∙ OMIM:610611 ∙ HGNC:28226 ∙ Uniprot:Q9BRT9 ∙ 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 GINS4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GINS4 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in GINS4

This is a list of pathogenic ClinVar variants found in the GINS4 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-41530209-G-A		not specified	Uncertain significance (Feb 16, 2023)
8-41530282-T-C		not specified	Uncertain significance (Oct 12, 2021)
8-41536413-T-G		not specified	Uncertain significance (Nov 15, 2023)
8-41537223-G-C		not specified	Uncertain significance (Oct 16, 2023)
8-41537252-C-T		not specified	Uncertain significance (Jan 30, 2024)
8-41537288-A-C		not specified	Uncertain significance (Dec 18, 2023)
8-41539729-G-A		not specified	Uncertain significance (Nov 13, 2023)
8-41539751-C-T		not specified	Uncertain significance (Dec 22, 2023)
8-41539774-G-A		not specified	Uncertain significance (Oct 03, 2022)
8-41539968-C-G		not specified	Uncertain significance (Dec 14, 2023)
8-41539992-C-A		not specified	Uncertain significance (Dec 19, 2023)
8-41541820-G-A		not specified	Uncertain significance (Aug 23, 2021)
8-41542007-C-A		not specified	Uncertain significance (Feb 22, 2023)
8-41542071-C-T		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GINS4	protein_coding	protein_coding	ENST00000276533	7	15841

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000137	0.867	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.538	111	128	0.866	0.00000711	1475
Missense in Polyphen		23	30.35	0.75782		322
Synonymous	1.10	38	47.6	0.798	0.00000274	410
Loss of Function	1.37	8	13.4	0.596	6.67e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000645	0.000645
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.000217	0.000217
South Asian	0.000360	0.000359
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. GINS4 is important for GINS complex assembly. 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: 0.147

Intolerance Scores

• loftool: 0.411
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.319
• hipred: Y
• hipred_score: 0.800
• ghis: 0.690

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.957

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gins4
• 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); neoplasm; cellular phenotype

Gene ontology

• Biological process: double-strand break repair via break-induced replication;inner cell mass cell proliferation;DNA strand elongation involved in DNA replication;DNA duplex unwinding
• Cellular component: GINS complex;nucleoplasm;cytoplasm;replication fork protection complex
• Molecular function: protein binding;3'-5' DNA helicase activity