HEATR9

Summary

HEATR9 (HEAT repeat containing 9, HGNC:26548) is a protein-coding gene on chromosome 17q12, encoding Protein HEATR9 (A2RTY3).

Predicted to act upstream of or within hematopoietic progenitor cell differentiation; response to cytokine; and response to virus.

Source: NCBI Gene 256957 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 85 total
• MANE Select transcript: NM_152781

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26548
Approved symbol	HEATR9
Name	HEAT repeat containing 9
Location	17q12
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32830
Ensembl gene	ENSG00000270379
Ensembl biotype	protein_coding
Entrez	256957

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 3 protein_coding, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000603218, ENST00000603323, ENST00000603852, ENST00000603870, ENST00000604376, ENST00000604400, ENST00000604834, ENST00000605080

RefSeq mRNA: 2 — MANE Select: NM_152781 NM_001321395, NM_152781

CCDS: CCDS11299, CCDS82108

Canonical transcript exons

ENST00000604834 — 15 exons

Exon	Start	End
ENSE00003494499	35856173	35856224
ENSE00003503557	35864497	35864553
ENSE00003505720	35858200	35858319
ENSE00003523801	35864758	35864890
ENSE00003537982	35854955	35855410
ENSE00003555067	35855664	35855750
ENSE00003561599	35863502	35863559
ENSE00003561807	35862995	35863125
ENSE00003575384	35865215	35865396
ENSE00003576734	35868655	35868891
ENSE00003596365	35856732	35856805
ENSE00003629593	35858433	35858525
ENSE00003640567	35864246	35864302
ENSE00003644828	35858888	35859070
ENSE00003659413	35866724	35866773

Expression profiles

Bgee: expression breadth broad, 98 present calls, max score 77.37.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0391 / max 40.1466, expressed in 5 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
165392	0.0153	3
165394	0.0136	4
165391	0.0059	3
165393	0.0043	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	77.37	gold quality
testis	UBERON:0000473	77.11	gold quality
granulocyte	CL:0000094	76.21	gold quality
right testis	UBERON:0004534	75.65	gold quality
blood	UBERON:0000178	62.71	gold quality
spleen	UBERON:0002106	58.32	gold quality
lymph node	UBERON:0000029	54.43	gold quality
bone marrow	UBERON:0002371	53.51	gold quality
duodenum	UBERON:0002114	53.20	gold quality
vermiform appendix	UBERON:0001154	53.04	gold quality
leukocyte	CL:0000738	51.93	gold quality
bone marrow cell	CL:0002092	51.63	gold quality
monocyte	CL:0000576	50.81	gold quality
small intestine Peyer’s patch	UBERON:0003454	49.94	gold quality
small intestine	UBERON:0002108	49.74	gold quality
mucosa of transverse colon	UBERON:0004991	49.16	gold quality
mucosa of stomach	UBERON:0001199	49.00	gold quality
tonsil	UBERON:0002372	48.65	gold quality
right lung	UBERON:0002167	48.42	gold quality
lower esophagus mucosa	UBERON:0035834	47.80	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	47.33	gold quality
lung	UBERON:0002048	45.51	gold quality
upper lobe of left lung	UBERON:0008952	45.42	gold quality
urinary bladder	UBERON:0001255	45.15	gold quality
rectum	UBERON:0001052	44.70	gold quality
gall bladder	UBERON:0002110	44.52	gold quality
cerebellum	UBERON:0002037	44.24	silver quality
cerebellar hemisphere	UBERON:0002245	44.18	silver quality
cerebellar cortex	UBERON:0002129	44.06	silver quality
right coronary artery	UBERON:0001625	43.92	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting HEATR9, 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-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-4451	98.82	68.17	1455
HSA-MIR-6754-5P	98.60	65.54	1627
HSA-MIR-6827-5P	98.46	64.88	1256
HSA-MIR-1236-5P	96.62	66.38	856
HSA-MIR-920	95.97	63.95	811
HSA-MIR-4300	95.85	64.56	1003
HSA-MIR-5591-5P	95.85	64.76	1002
HSA-MIR-6889-5P	90.26	64.13	291
HSA-MIR-6777-5P	88.76	62.64	222

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Heatr9	ENSMUSG00000018925
rattus_norvegicus	Heatr9	ENSRNOG00000037100

Protein

Protein identifiers

Protein HEATR9 — A2RTY3 (reviewed: A2RTY3)

Alternative names: HEAT repeat-containing protein 9

All UniProt accessions (3): A2RTY3, A0A075B7D1, A0A075B7D3

UniProt curated annotations — full annotation on UniProt →

Isoforms (5)

UniProt ID	Names	Canonical?
A2RTY3-1	1	yes
A2RTY3-2	2
A2RTY3-3	3
A2RTY3-4	4
A2RTY3-5	5

RefSeq proteins (2): NP_001308324, NP_689994* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011989	ARM-like	Homologous_superfamily
IPR016024	ARM-type_fold	Homologous_superfamily
IPR052873	HEATR9	Family

UniProt features (12 total): splice variant 6, sequence conflict 3, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A2RTY3-F1	70.40	0.43

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, GOBP_RESPONSE_TO_PEPTIDE, PTF1BETA_Q6, GOBP_RESPONSE_TO_VIRUS, CHICAS_RB1_TARGETS_CONFLUENT, MIR6827_5P, chr17q12, HOWARD_PBMC_INACT_MONOV_INFLUENZA_A_INDONESIA_05_2005_H5N1_AGE_19_39YO_AS03_ADJUVANT_VS_BUFFER_1DY_DN, GOBP_BIOLOGICAL_PROCESS_INVOLVED_IN_INTERSPECIES_INTERACTION_BETWEEN_ORGANISMS, WP_17Q12_COPY_NUMBER_VARIATION_SYNDROME, GOBP_HEMOPOIESIS, GSE22601_IMMATURE_CD4_SINGLE_POSITIVE_VS_DOUBLE_POSITIVE_THYMOCYTE_UP, GSE22601_DOUBLE_NEGATIVE_VS_CD8_SINGLE_POSITIVE_THYMOCYTE_UP, MCCABE_BOUND_BY_HOXC6, GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_6H_UP

GO Biological Process (3): hematopoietic progenitor cell differentiation (GO:0002244), response to virus (GO:0009615), response to cytokine (GO:0034097)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
hemopoiesis	1
cell differentiation	1
response to other organism	1
response to peptide	1
binding	1

Protein interactions and networks

STRING

448 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HEATR9	SERGEF	Q9UGK8	572
HEATR9	OR6T1	Q8NGN1	542
HEATR9	C5orf58	C9J3I9	507
HEATR9	CFAP184	Q2M329	506
HEATR9	GTSF1L	Q9H1H1	476
HEATR9	C20orf173	Q96LM9	475
HEATR9	IQCN	Q9H0B3	461
HEATR9	GAS2L2	Q8NHY3	451
HEATR9	CABS1	Q96KC9	448
HEATR9	FAM221A	A4D161	445
HEATR9	CRTAM	O95727	442
HEATR9	CCL16	O15467	435
HEATR9	TMCO5A	Q8N6Q1	429
HEATR9	ENTREP2	O60320	428
HEATR9	SPATA31G1	Q5VYM1	411

IntAct

5 interactions, top by confidence:

A	B	Type	Score
HEATR9	HEMK1	psi-mi:“MI:0915”(physical association)	0.560
HEATR9	H2BC21	psi-mi:“MI:0915”(physical association)	0.400
HEMK1	HEATR9	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): HEATR9 (Two-hybrid), HIST2H2BE (Proximity Label-MS), HNRNPA2B1 (Cross-Linking-MS (XL-MS)), HEATR9 (Cross-Linking-MS (XL-MS)), HNRNPC (Cross-Linking-MS (XL-MS)), HEATR9 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A0M3U1B0, A1A5Q6, A2AFS9, A2AVR2, A2CI98, A2CJ06, A2RTY3, A2RUW0, O70167, O70173, P0C2Y1, P15304, P59729, Q08EC4, Q3SYK4, Q3TYG6, Q3U1D0, Q4R744, Q4R9E9, Q5R4B2, Q5T4T6, Q5TGP6, Q5VWK0, Q68CQ1, Q6AYJ3, Q6IFT4, Q6IRU7, Q6REY9, Q6ZUA9, Q7Z572, Q80VH0, Q86WZ0, Q86XG9, Q8C0X8, Q8CCC3, Q8ND61, Q8NDZ2, Q8TB24, Q96M43, Q96QP1

Diamond homologs: A2RTY3, Q4R744, Q5QNV8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	74
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2065 predictions. Top by Δscore:

Variant	Effect	Δscore
17:35855658:A:AC	donor_gain	1.0000
17:35855659:C:CC	donor_gain	1.0000
17:35855663:CA:C	donor_gain	1.0000
17:35856730:A:AC	donor_gain	1.0000
17:35856731:C:CC	donor_gain	1.0000
17:35856731:CG:C	donor_gain	1.0000
17:35864217:T:A	donor_gain	1.0000
17:35864571:CCAG:C	acceptor_gain	1.0000
17:35864572:C:CT	acceptor_gain	1.0000
17:35864572:C:T	acceptor_gain	1.0000
17:35864573:A:T	acceptor_gain	1.0000
17:35864574:G:C	acceptor_gain	1.0000
17:35864574:G:GC	acceptor_gain	1.0000
17:35865217:A:AC	donor_gain	1.0000
17:35865218:C:CC	donor_gain	1.0000
17:35865218:CAGT:C	donor_gain	1.0000
17:35865230:ATTTT:A	donor_gain	1.0000
17:35865234:T:A	donor_gain	1.0000
17:35865255:C:CA	donor_gain	1.0000
17:35865260:T:A	donor_gain	1.0000
17:35855662:A:AC	donor_gain	0.9900
17:35855663:C:CC	donor_gain	0.9900
17:35855663:CACT:C	donor_gain	0.9900
17:35855747:CACC:C	acceptor_gain	0.9900
17:35855749:CC:C	acceptor_gain	0.9900
17:35855750:CC:C	acceptor_gain	0.9900
17:35855751:C:CA	acceptor_loss	0.9900
17:35855752:T:A	acceptor_loss	0.9900
17:35856171:A:AC	donor_gain	0.9900
17:35856172:C:CC	donor_gain	0.9900

AlphaMissense

3751 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:35856187:C:G	A422P	0.983
17:35858307:C:G	A349P	0.980
17:35864549:A:G	L153P	0.964
17:35864302:C:G	A171P	0.962
17:35858986:C:G	A281P	0.960
17:35858977:A:G	C284R	0.958
17:35863038:A:G	L238P	0.958
17:35858294:A:T	L353H	0.956
17:35858294:A:G	L353P	0.953
17:35858315:C:G	R346P	0.953
17:35859030:A:G	L266P	0.950
17:35856797:C:A	R387S	0.949
17:35856797:C:G	R387S	0.949
17:35858983:C:G	A282P	0.944
17:35856195:C:G	R419P	0.943
17:35856219:A:G	L411P	0.942
17:35858966:G:C	F287L	0.937
17:35858966:G:T	F287L	0.937
17:35858968:A:G	F287L	0.937
17:35858203:G:C	F383L	0.935
17:35858203:G:T	F383L	0.935
17:35858205:A:G	F383L	0.935
17:35858231:A:G	L374P	0.935
17:35858975:G:C	C284W	0.935
17:35856186:G:T	A422E	0.933
17:35858973:A:G	L285P	0.932
17:35855409:A:G	L456P	0.931
17:35864298:A:G	L172P	0.931
17:35864764:T:A	R149S	0.931
17:35864764:T:G	R149S	0.931

dbSNP variants (sampled 300 via entrez): RS1000061814 (17:35866256 C>T), RS1000478954 (17:35858319 C>T), RS1000560836 (17:35868823 G>A), RS1000672597 (17:35864659 T>G), RS1000902682 (17:35855668 T>C), RS1000945024 (17:35867104 A>C), RS1001053830 (17:35861254 C>G,T), RS1001520075 (17:35856857 A>G), RS1001550819 (17:35865461 G>A), RS1001768001 (17:35869968 C>A,T), RS1001854885 (17:35854649 TGGG>T,TGG,TGGGG), RS1002004911 (17:35860346 T>C,G), RS1002076576 (17:35863273 G>A,T), RS1002178427 (17:35868343 C>T), RS1002521285 (17:35855306 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases abundance, decreases expression	1
Diuron	decreases expression	1
Lipopolysaccharides	increases expression, affects response to substance, affects cotreatment	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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