GIN1

gypsy retrotransposon integrase 1

Basic information

Region (hg38): 5:103086000-103120138

Previous symbols: [ "ZH2C2" ]

Links

ENSG00000145723 ∙ NCBI:54826 ∙ ∙ HGNC:25959 ∙ Uniprot:Q9NXP7 ∙ 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 GIN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GIN1 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			33	3	1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	3	1

Variants in GIN1

This is a list of pathogenic ClinVar variants found in the GIN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-103087920-T-C		not specified	Uncertain significance (Dec 12, 2024)
5-103088013-A-G		not specified	Uncertain significance (Jul 11, 2023)
5-103088082-A-G		not specified	Uncertain significance (Sep 10, 2024)
5-103088088-G-T		not specified	Uncertain significance (Dec 26, 2023)
5-103088106-G-A		not specified	Uncertain significance (Oct 30, 2023)
5-103088124-A-G		not specified	Uncertain significance (Sep 27, 2021)
5-103088125-T-C		not specified	Uncertain significance (Jun 24, 2022)
5-103088137-C-T		not specified	Uncertain significance (Jan 02, 2024)
5-103088151-C-A		not specified	Uncertain significance (Jun 30, 2022)
5-103088166-A-T		not specified	Uncertain significance (May 04, 2023)
5-103096588-A-G		not specified	Uncertain significance (Sep 01, 2021)
5-103096639-C-G		not specified	Uncertain significance (Sep 27, 2021)
5-103096651-T-C		not specified	Uncertain significance (Dec 26, 2023)
5-103096690-C-T		not specified	Uncertain significance (Oct 17, 2024)
5-103096714-C-G		not specified	Uncertain significance (Dec 20, 2021)
5-103096730-C-T		not specified	Uncertain significance (Jan 08, 2025)
5-103096763-G-C		not specified	Uncertain significance (Dec 16, 2024)
5-103096784-T-C		not specified	Uncertain significance (Dec 27, 2023)
5-103096809-C-G		not specified	Likely benign (Jun 10, 2024)
5-103096813-T-C		not specified	Uncertain significance (Jul 25, 2023)
5-103097369-T-C		not specified	Likely benign (Apr 29, 2024)
5-103097378-T-C		not specified	Likely benign (Mar 13, 2023)
5-103097408-A-C		not specified	Uncertain significance (Oct 12, 2021)
5-103097450-C-T		not specified	Uncertain significance (Apr 01, 2024)
5-103097483-G-T		not specified	Uncertain significance (Nov 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GIN1	protein_coding	protein_coding	ENST00000399004	7	34152

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000242	0.982	124742	0	35	124777	0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.391	244	262	0.932	0.0000122	3457
Missense in Polyphen		37	44.923	0.82363		567
Synonymous	-0.765	101	91.7	1.10	0.00000440	957
Loss of Function	2.13	11	21.7	0.507	0.00000107	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000147	0.000147
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.000112	0.000111
Finnish	0.000246	0.000232
European (Non-Finnish)	0.000162	0.000159
Middle Eastern	0.000112	0.000111
South Asian	0.000113	0.0000980
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.624
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.353
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.857

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gin1

Gene ontology

• Biological process: DNA integration
• Molecular function: nucleic acid binding