GIN1

protein-coding

gypsy retrotransposon integrase 1

Gene summary

Predicted to enable nucleic acid binding activity. Predicted to be involved in DNA integration. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZH2C2

MANE transcript

NM_017676.2

Inheritance

—

ClinVar variants

U:65B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr5:103,086,000-103,120,138

External References & Databases

Ensembl (ENSG00000145723)

Transcript & Mutation Effects

hg38 • Region Span ~34.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GIN1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 65

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017676.2. 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			63 clinvar	4 clinvar		67
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	65	4	0	69

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017676.2	RefSeq	NP_060146.2	7	MANE Select
ENST00000399004.7	Ensembl	ENSP00000381970.2	7	MANE Select
NM_001317954.2	RefSeq	NP_001304883.1	5	Standard
ENST00000508629.5	Ensembl	ENSP00000427162.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

DNA integration

Molecular Function

nucleic acid binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000399004
Coding exons: 7
Length: 34152
Individuals with no LoFs: 124742
Homozygous LoFs: 0
Heterozygous LoFs: 35
Defined: 124777
p: 0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.391	244	262	0.932	0.0000122	3457
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00025	0.00023	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00011	0.000098	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.136

Intolerance Scores

LoFtool: 0.624
RVIS EVS: 0.6
RVIS percentile EVS: 82.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.857

Gene Damage Prediction

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