GINS2

protein-coding

GINS complex subunit 2, the group of GINS complex

Gene summary

The yeast heterotetrameric GINS complex is made up of Sld5 (GINS4; MIM 610611), Psf1 (GINS1; MIM 610608), Psf2, and Psf3 (GINS3; MIM 610610). The formation of this complex is essential for the initiation of DNA replication in yeast and Xenopus egg extracts (Ueno et al., 2005 [PubMed 16287864]). See GINS1 for additional information about the GINS complex.[supplied by OMIM, Mar 2008]

MANE transcript

NM_016095.3

Inheritance

ClinVar variants

U:59B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.18

Max pathogenic AF

—

Genomic locus

chr16:85,676,198-85,690,073

External References & Databases

Ensembl (ENSG00000131153)

Transcript & Mutation Effects

hg38 • Region Span ~13.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Meier-Gorlin syndromeLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0016817

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GINS2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 56

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016095.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			58 clinvar			58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	59	1	0	60

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016095.3	RefSeq	NP_057179.1	5	MANE Select
ENST00000253462.8	Ensembl	ENSP00000253462.3	5	MANE Select
ENST00000595355.5	Ensembl	ENSP00000470984.1	3	Standard
ENST00000596233.1	Ensembl	ENSP00000469346.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Unwinding of DNA
DNA Replication
DNA strand elongation
Synthesis of DNA
S Phase

Biological Process

double-strand break repair via break-induced replication
DNA strand elongation involved in DNA replication
DNA duplex unwinding

Molecular Function

protein binding
3'-5' DNA helicase activity

Cellular Component

GINS complex
nucleoplasm
replication fork protection complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000253462
Coding exons: 5
Length: 13876
Individuals with no LoFs: 125708
Homozygous LoFs: 0
Heterozygous LoFs: 40
Defined: 125748
p: 0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.32	138	101	1.37	0.00000560	1209
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00039	0.00038	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00022	0.00020	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.136

Intolerance Scores

LoFtool: 0.451
RVIS EVS: -0.74
RVIS percentile EVS: 13.94

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.802

Gene Damage Prediction

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