HARBI1

Summary

HARBI1 (harbinger transposase derived 1, HGNC:26522) is a protein-coding gene on chromosome 11p11.2, encoding Putative nuclease HARBI1 (Q96MB7). Transposase-derived protein that may have nuclease activity (Potential).

Predicted to enable metal ion binding activity and nuclease activity. Located in centriolar satellite; cytosol; and plasma membrane.

Source: NCBI Gene 283254 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 51 total
• MANE Select transcript: NM_173811

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26522
Approved symbol	HARBI1
Name	harbinger transposase derived 1
Location	11p11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32675
Ensembl gene	ENSG00000180423
Ensembl biotype	protein_coding
OMIM	615086
Entrez	283254

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 protein_coding

ENST00000326737, ENST00000529192, ENST00000532281, ENST00000891261, ENST00000891262, ENST00000936938, ENST00000936939, ENST00000936940, ENST00000936941, ENST00000960128, ENST00000960129, ENST00000960130

RefSeq mRNA: 1 — MANE Select: NM_173811 NM_173811

CCDS: CCDS7920

Canonical transcript exons

ENST00000326737 — 3 exons

Exon	Start	End
ENSE00001230377	46617124	46617227
ENSE00001230390	46615568	46616381
ENSE00001415616	46602861	46603909

Expression profiles

Bgee: expression breadth ubiquitous, 171 present calls, max score 84.40.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.1454 / max 139.9218, expressed in 1612 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
119526	1.9761	1283
119525	1.1443	488
119527	1.0249	358

Top tissues by expression

245 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.40	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.24	gold quality
sperm	CL:0000019	82.03	silver quality
bone marrow cell	CL:0002092	79.30	gold quality
islet of Langerhans	UBERON:0000006	77.96	gold quality
left testis	UBERON:0004533	77.74	gold quality
right testis	UBERON:0004534	77.74	gold quality
stromal cell of endometrium	CL:0002255	77.26	gold quality
testis	UBERON:0000473	76.94	gold quality
cortical plate	UBERON:0005343	75.69	gold quality
monocyte	CL:0000576	75.14	gold quality
leukocyte	CL:0000738	75.00	gold quality
prefrontal cortex	UBERON:0000451	73.58	gold quality
smooth muscle tissue	UBERON:0001135	72.21	gold quality
ventricular zone	UBERON:0003053	72.07	gold quality
ganglionic eminence	UBERON:0004023	71.80	gold quality
right adrenal gland	UBERON:0001233	71.76	gold quality
right adrenal gland cortex	UBERON:0035827	71.70	gold quality
rectum	UBERON:0001052	71.44	gold quality
granulocyte	CL:0000094	71.40	gold quality
kidney epithelium	UBERON:0004819	70.73	gold quality
gastrocnemius	UBERON:0001388	70.72	gold quality
bone marrow	UBERON:0002371	70.38	gold quality
left adrenal gland	UBERON:0001234	70.32	gold quality
muscle of leg	UBERON:0001383	70.27	gold quality
pancreas	UBERON:0001264	69.92	gold quality
lymph node	UBERON:0000029	69.68	gold quality
left adrenal gland cortex	UBERON:0035825	69.48	gold quality
mucosa of transverse colon	UBERON:0004991	69.36	gold quality
adrenal cortex	UBERON:0001235	69.35	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting HARBI1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-10395-5P	99.86	67.35	676
HSA-MIR-29B-2-5P	99.67	68.98	1726
HSA-MIR-5700	99.64	69.88	2280
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-892A	99.54	68.16	1141
HSA-MIR-520E-5P	99.27	68.90	1513
HSA-MIR-4264	96.35	64.76	1480

Literature-anchored findings (GeneRIF, showing 1)

• The functions of two transposon-derived human proteins: HARBI1, a domesticated transposase-derived protein, and NAIF1, which contains a trihelix motif similar to that described in the Myb-like protein, was investigated. (PMID:18339812)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	harbi1	ENSDARG00000036038
mus_musculus	Harbi1	ENSMUSG00000027243
rattus_norvegicus	Harbi1	ENSRNOG00000081861
drosophila_melanogaster	CG43088	FBGN0262534

Protein

Protein identifiers

Putative nuclease HARBI1 — Q96MB7 (reviewed: Q96MB7)

Alternative names: Harbinger transposase-derived nuclease

All UniProt accessions (3): Q96MB7, E9PK24, E9PQI1

UniProt curated annotations — full annotation on UniProt →

Function. Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity.

Subunit / interactions. Interacts with NAIF1.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Detected in brain, eye, nerve tissue, kidney and lung.

Similarity. Belongs to the HARBI1 family.

RefSeq proteins (1): NP_776172* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026103	HARBI1_animal	Family
IPR027806	HARBI1_dom	Domain
IPR045249	HARBI1-like	Family

Pfam: PF13359

UniProt features (6 total): binding site 4, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96MB7-F1	84.96	0.64

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (4): 149; 199; 225; 261

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 71 (showing top): GOMF_NUCLEASE_ACTIVITY, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GGGTGGRR_PAX4_03, TGANTCA_AP1_C, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, HSF1_01, ARID5B_TARGET_GENES, BARX1_TARGET_GENES, DIDO1_TARGET_GENES, DMRT1_TARGET_GENES, ELF2_TARGET_GENES, GUCY1B1_TARGET_GENES, KLF7_TARGET_GENES, NFE2L1_TARGET_GENES, RFX7_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (4): nuclease activity (GO:0004518), hydrolase activity (GO:0016787), metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), cytosol (GO:0005829), plasma membrane (GO:0005886), centriolar satellite (GO:0034451), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
catalytic activity, acting on a nucleic acid	1
catalytic activity	1
cation binding	1
binding	1
intracellular membrane-bounded organelle	1
cytoplasm	1
membrane	1
cell periphery	1
centrosome	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

306 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HARBI1	NAIF1	Q69YI7	801
HARBI1	PGBD5	Q8N414	663
HARBI1	GIN1	Q9NXP7	592
HARBI1	THAP9	Q9H5L6	589
HARBI1	QRICH1	Q2TAL8	548
HARBI1	TIGD2	Q4W5G0	517
HARBI1	PIGZ	Q86VD9	505
HARBI1	PRORP	O15091	487
HARBI1	POGK	Q9P215	479
HARBI1	PGBD2	Q6P3X8	445
HARBI1	SHPK	Q9UHJ6	433
HARBI1	ZBED8	Q8IZ13	433
HARBI1	CENPBD1P	B2RD01	431
HARBI1	SFT2D2	O95562	430
HARBI1	TIGD5	Q53EQ6	397

IntAct

3 interactions, top by confidence:

A	B	Type	Score
HARBI1	NAIF1	psi-mi:“MI:0915”(physical association)	0.590

BioGRID (3): NAIF1 (Affinity Capture-MS), NAIF1 (Affinity Capture-MS), HARBI1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2K1Q8, B0BN95, B2RRL2, O14423, O43422, O46510, O60108, O75564, O96006, P49777, P55205, P55211, Q01841, Q0VBL1, Q17QR8, Q17RP2, Q3V1F8, Q4W5G0, Q5U538, Q5XH12, Q60976, Q62711, Q66KB7, Q6AZB8, Q6B0B8, Q6IE26, Q6NT04, Q6P7F1, Q7L775, Q7L7V1, Q7TM95, Q8BR93, Q8BUZ3, Q8BZS9, Q8IY51, Q8K3R3, Q8VEH5, Q924H9, Q94K49, Q96DM1

Diamond homologs: B0BN95, Q17QR8, Q5U538, Q6AZB8, Q8BR93, Q96MB7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

51 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	46
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

540 predictions. Top by Δscore:

Variant	Effect	Δscore
11:46603910:C:CA	acceptor_loss	0.9900
11:46617183:T:TA	donor_gain	0.9900
11:46617886:CGCAG:C	donor_loss	0.9900
11:46617888:CAG:C	donor_loss	0.9900
11:46617889:AG:A	donor_loss	0.9900
11:46617890:GGT:G	donor_loss	0.9900
11:46617891:G:A	donor_loss	0.9900
11:46617892:T:G	donor_loss	0.9900
11:46615840:T:TA	donor_gain	0.9800
11:46603882:C:CT	acceptor_gain	0.9700
11:46617156:TCCC:T	donor_gain	0.9700
11:46603907:CAC:C	acceptor_gain	0.9600
11:46617813:G:GT	donor_gain	0.9600
11:46603910:C:CC	acceptor_gain	0.9500
11:46615561:AACTT:A	donor_loss	0.9500
11:46615562:ACTTA:A	donor_loss	0.9500
11:46615563:CTTAC:C	donor_loss	0.9500
11:46615564:TTA:T	donor_loss	0.9500
11:46615565:TA:T	donor_loss	0.9500
11:46615566:A:AA	donor_loss	0.9500
11:46617157:C:A	donor_gain	0.9500
11:46615566:AC:A	donor_gain	0.9400
11:46615567:CC:C	donor_gain	0.9400
11:46617156:T:TA	donor_gain	0.9400
11:46615566:A:AC	donor_gain	0.9300
11:46615567:C:CC	donor_gain	0.9300
11:46616125:A:C	donor_gain	0.9300
11:46617186:T:TA	donor_gain	0.9300
11:46615609:CTA:C	donor_gain	0.9100
11:46603924:C:T	acceptor_gain	0.9000

AlphaMissense

2304 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:46603767:G:C	F271L	0.997
11:46603767:G:T	F271L	0.997
11:46603769:A:G	F271L	0.997
11:46616001:A:C	F79L	0.997
11:46616001:A:T	F79L	0.997
11:46616003:A:G	F79L	0.997
11:46615950:A:C	S96R	0.996
11:46615950:A:T	S96R	0.996
11:46615952:T:G	S96R	0.996
11:46615927:A:T	V104D	0.995
11:46615931:A:G	C103R	0.995
11:46615947:C:A	Q97H	0.995
11:46615947:C:G	Q97H	0.995
11:46615983:G:C	F85L	0.995
11:46615983:G:T	F85L	0.995
11:46615985:A:G	F85L	0.995
11:46615933:C:G	R102P	0.994
11:46616011:G:T	A76E	0.994
11:46616014:G:T	A75E	0.994
11:46603695:A:C	C295W	0.993
11:46615915:G:A	T108I	0.993
11:46615943:A:G	S99P	0.993
11:46615951:C:A	S96I	0.993
11:46615980:C:A	Q86H	0.993
11:46615980:C:G	Q86H	0.993
11:46616002:A:G	F79S	0.993
11:46615721:A:G	S173P	0.992
11:46615918:A:T	V107D	0.992
11:46616000:A:C	Y80D	0.992
11:46603690:A:T	V297D	0.991

dbSNP variants (sampled 300 via entrez): RS1000020603 (11:46614527 G>A), RS1000138243 (11:46608096 T>C), RS1000194244 (11:46617167 C>T), RS1000341024 (11:46607442 GCAT>G), RS1000394734 (11:46607170 GAAAA>G), RS1000620647 (11:46612637 A>C), RS1000734782 (11:46605486 G>A,C,T), RS1000798452 (11:46606068 T>C), RS1000824311 (11:46618213 C>T), RS1000952883 (11:46617861 G>A), RS1001069041 (11:46618206 A>G), RS1001295101 (11:46610716 CA>C), RS1002194106 (11:46603148 A>T), RS1002226534 (11:46603471 G>C), RS1002356829 (11:46604279 C>T)

Disease associations

OMIM: gene MIM:615086 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST000763_2	Immunoglobulin A	2.000000e-06
GCST004521_122	Autism spectrum disorder or schizophrenia	3.000000e-13
GCST004521_165	Autism spectrum disorder or schizophrenia	3.000000e-08
GCST006803_20	Schizophrenia	3.000000e-13
GCST006947_1	Feeling fed-up	3.000000e-10
GCST007825_4	Alzheimer’s disease or fasting glucose levels (pleiotropy)	3.000000e-16
GCST009600_131	Anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, or Tourette syndrome (pleiotropy)	1.000000e-08
GCST90000047_168	Age at first sexual intercourse	2.000000e-10

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004747	protein measurement
EFO:0009588	feeling “fed-up” measurement
EFO:0009749	age at first sexual intercourse measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
kojic acid	decreases expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
Sunitinib	increases expression	1
Benzo(a)pyrene	increases mutagenesis	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Urethane	increases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_SQ89	HAP1 HARBI1 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.