REPIN1

protein-coding

replication initiator 1, the group of Zinc fingers C2H2-type

Gene summary

Enables sequence-specific DNA binding activity. Predicted to be involved in regulation of fatty acid transport and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of D-glucose import across plasma membrane. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNF464

MANE transcript

NM_001099695.2

Inheritance

—

ClinVar variants

U:106B:6

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr7:150,368,189-150,374,044

External References & Databases

Ensembl (ENSG00000214022)

Transcript & Mutation Effects

hg38 • Region Span ~5.9 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 REPIN1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 108

not providedTotal: 2

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001099695.2. 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			105 clinvar	5 clinvar		110
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	106	6	0	112

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 74 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001099695.2	RefSeq	NP_001093165.1	2	MANE Select
ENST00000489432.7	Ensembl	ENSP00000417291.2	2	MANE Select
NM_001099696.3	RefSeq	NP_001093166.1	1	Standard
NM_001362745.2	RefSeq	NP_001349674.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

DNA replication

Molecular Function

DNA binding
RNA binding
metal ion binding

Cellular Component

nucleus
nuclear origin of replication recognition complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000489432
Coding exons: 2
Length: 5856
Individuals with no LoFs: 125279
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125293
p: 0.0000559

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.43	295	438	0.673	0.0000337	3912
Missense (PolyPhen)		115	224.5	0.51225		1965
Synonymous	1.15	172	192	0.895	0.0000147	1338
Loss of Function	3.16	6	22.0	0.273	0.00000149	184

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.00011	0.000093	rare
European (Non-Finnish)	0.000063	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Sequence-specific double-stranded DNA-binding protein required for initiation of chromosomal DNA replication. Binds on 5'-ATT-3' reiterated sequences downstream of the origin of bidirectional replication (OBR) and a second, homologous ATT sequence of opposite orientation situated within the OBR zone. Facilitates DNA bending.;

Intolerance Scores

LoFtool: 0.482
RVIS EVS: 0.93
RVIS percentile EVS: 89.79

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.915

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High