HARBI1

protein-coding

harbinger transposase derived 1, the group of DNA transposon derived genes

Gene summary

Predicted to enable hydrolase activity; metal ion binding activity; and nuclease activity. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C11orf77

MANE transcript

NM_173811.4

Inheritance

—

ClinVar variants

U:48B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr11:46,602,861-46,617,909

External References & Databases

Ensembl (ENSG00000180423)

Transcript & Mutation Effects

hg38 • Region Span ~15.0 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 HARBI1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 48

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173811.4. 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						0
missense			48 clinvar	2 clinvar		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	2	0	50

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173811.4	RefSeq	NP_776172.1	2	MANE Select
ENST00000326737.3	Ensembl	ENSP00000317743.3	2	MANE Select
ENST00000529192.1	Ensembl	ENSP00000431697.1	1	Standard
ENST00000532281.1	Ensembl	ENSP00000436232.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

nucleic acid phosphodiester bond hydrolysis

Molecular Function

nuclease activity
metal ion binding

Cellular Component

nucleus
microtubule organizing center
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000326737
Coding exons: 2
Length: 15049
Individuals with no LoFs: 125694
Homozygous LoFs: 0
Heterozygous LoFs: 54
Defined: 125748
p: 0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.365	193	208	0.929	0.0000117	2299
Missense (PolyPhen)		61	79.871	0.76373		874
Synonymous	-1.15	86	73.5	1.17	0.00000373	704
Loss of Function	1.54	7	13.0	0.538	9.61e-7	122

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00030	0.00030	rare
South Asian	0.000065	0.000065	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity. {ECO:0000269|PubMed:15169610, ECO:0000269|PubMed:18339812, ECO:0000305}.;

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.329
RVIS EVS: -0.63
RVIS percentile EVS: 17.03

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.136

Gene Damage Prediction

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