HRCT1

Summary

HRCT1 (histidine rich carboxyl terminus 1, HGNC:33872) is a protein-coding gene on chromosome 9p13.3, encoding Histidine-rich carboxyl terminus protein 1 (Q6UXD1).

Predicted to be located in membrane.

Source: NCBI Gene 646962 — RefSeq curated summary.

At a glance

• GWAS associations: 40
• Clinical variants (ClinVar): 61 total
• MANE Select transcript: NM_001039792

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33872
Approved symbol	HRCT1
Name	histidine rich carboxyl terminus 1
Location	9p13.3
Locus type	gene with protein product
Status	Approved
Aliases	LGLL338, PRO537, UNQ338
Ensembl gene	ENSG00000196196
Ensembl biotype	protein_coding
OMIM	621339
Entrez	646962

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000354323

RefSeq mRNA: 1 — MANE Select: NM_001039792 NM_001039792

CCDS: CCDS35012

Canonical transcript exons

ENST00000354323 — 1 exons

Exon	Start	End
ENSE00001408309	35906202	35907136

Expression profiles

Bgee: expression breadth ubiquitous, 162 present calls, max score 96.88.

FANTOM5 (CAGE): breadth broad, TPM avg 1.8570 / max 68.1361, expressed in 649 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
96644	1.2429	528
96645	0.4457	235
96643	0.1232	50
205477	0.0453	17

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	96.88	gold quality
right coronary artery	UBERON:0001625	92.78	gold quality
descending thoracic aorta	UBERON:0002345	92.31	gold quality
popliteal artery	UBERON:0002250	92.14	gold quality
tibial artery	UBERON:0007610	92.10	gold quality
aorta	UBERON:0000947	91.80	gold quality
ascending aorta	UBERON:0001496	91.44	gold quality
thoracic aorta	UBERON:0001515	91.43	gold quality
coronary artery	UBERON:0001621	89.90	gold quality
left coronary artery	UBERON:0001626	89.89	gold quality
upper arm skin	UBERON:0004263	89.61	gold quality
ileal mucosa	UBERON:0000331	87.49	gold quality
subcutaneous adipose tissue	UBERON:0002190	86.95	gold quality
transverse colon	UBERON:0001157	85.66	gold quality
adipose tissue	UBERON:0001013	85.55	gold quality
saphenous vein	UBERON:0007318	84.31	silver quality
layer of synovial tissue	UBERON:0007616	84.15	gold quality
lower esophagus muscularis layer	UBERON:0035833	82.68	gold quality
mucosa of stomach	UBERON:0001199	82.55	gold quality
lower esophagus	UBERON:0013473	82.53	gold quality
synovial joint	UBERON:0002217	82.43	silver quality
adipose tissue of abdominal region	UBERON:0007808	82.37	gold quality
omental fat pad	UBERON:0010414	81.99	gold quality
peritoneum	UBERON:0002358	81.97	gold quality
colonic mucosa	UBERON:0000317	80.84	gold quality
large intestine	UBERON:0000059	80.48	gold quality
colon	UBERON:0001155	80.45	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	79.82	gold quality
rectum	UBERON:0001052	79.11	gold quality
intestine	UBERON:0000160	78.97	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	22.63
E-ANND-3	yes	6.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting HRCT1, 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-4283	100.00	66.42	2097
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-140-5P	99.44	67.20	792
HSA-MIR-103A-1-5P	99.39	67.78	1545
HSA-MIR-103A-2-5P	99.39	67.72	1577
HSA-MIR-4460	99.37	68.52	615
HSA-MIR-6728-3P	98.63	67.63	1534
HSA-MIR-615-5P	98.10	63.76	591
HSA-MIR-6802-3P	97.29	65.42	613
HSA-MIR-6760-3P	96.35	68.31	1001

Literature-anchored findings (GeneRIF, showing 1)

• HRCT1, negatively regulated by miR-124-3p, promotes tumor metastasis and the growth of gastric cancer by activating the ERBB2-MAPK pathway. (PMID:36602696)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Hrct1	ENSMUSG00000071001
rattus_norvegicus	Hrct1	ENSRNOG00000039336

Protein

Protein identifiers

Histidine-rich carboxyl terminus protein 1 — Q6UXD1 (reviewed: Q6UXD1)

All UniProt accessions (1): Q6UXD1

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001034881* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031506	HRCT1	Family

Pfam: PF15758

UniProt features (4 total): chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UXD1-F1	62.62	0.13

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 53 (showing top): PATIL_LIVER_CANCER, chr9p13, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN, LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_UP, E2F2_TARGET_GENES, GREB1_TARGET_GENES, GUCY1B1_TARGET_GENES, HDAC4_TARGET_GENES, ID2_TARGET_GENES, IGLV5_37_TARGET_GENES, KMT2D_TARGET_GENES, TEAD2_TARGET_GENES, ZNF30_TARGET_GENES, ZNF7_TARGET_GENES, MIR6802_3P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

330 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HRCT1	SPAAR	A0A1B0GVQ0	605
HRCT1	MYO15B	Q96JP2	560
HRCT1	CCDC177	Q9NQR7	531
HRCT1	OR4L1	Q8NH43	490
HRCT1	A0A0G2JMU2	A0A0G2JMU2	479
HRCT1	POTEB3	A0JP26	475
HRCT1	FOXN4	Q96NZ1	447
HRCT1	SERTAD2	Q14140	447
HRCT1	FRG2B	Q96QU4	419
HRCT1	ESX1	Q8N693	406
HRCT1	ZNF701	Q9NV72	399
HRCT1	AP5S1	Q9NUS5	396
HRCT1	OR2I1	Q8NGU4	389
HRCT1	FAM180B	Q6P0A1	383
HRCT1	NTM	Q9P121	379

IntAct

0 interactions, top by confidence:

BioGRID (1): HRCT1 (PCA)

ESM2 similar proteins: A7XCE1, A7XCE8, D5L5Q8, O77645, O97965, P04554, P06841, P07978, P08433, P0DPG6, P11101, P11248, P11378, P13275, P19757, P22613, P26377, P29258, P34084, P35297, P35298, P35299, P35300, P35301, P35303, P35306, P35308, P35309, P35310, P35312, P35313, P35314, P42147, P56620, P61253, P83055, Q09821, Q0P670, Q17RF5, Q28337

Diamond homologs: Q6UXD1, Q9D6B9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	50
Likely benign	11
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

343 predictions. Top by Δscore:

Variant	Effect	Δscore
9:35906399:G:GT	donor_gain	0.8400
9:35906244:GGA:G	donor_gain	0.8300
9:35906245:GAG:G	donor_gain	0.8300
9:35906391:G:GT	donor_gain	0.7900
9:35906416:G:GT	donor_gain	0.7600
9:35906417:A:T	donor_gain	0.7600
9:35906400:A:T	donor_gain	0.7400
9:35906433:G:GT	donor_gain	0.7300
9:35906427:C:G	donor_gain	0.7200
9:35906237:G:T	donor_gain	0.6900
9:35906247:G:GG	donor_gain	0.6900
9:35906423:AC:A	donor_gain	0.6900
9:35906530:T:G	donor_gain	0.6800
9:35906412:A:T	donor_gain	0.6700
9:35906246:A:AG	donor_gain	0.6300
9:35906252:G:T	donor_gain	0.6300
9:35906271:G:T	donor_gain	0.6300
9:35906420:C:G	donor_gain	0.6300
9:35906953:GA:G	acceptor_gain	0.6300
9:35906214:GGC:G	donor_gain	0.6100
9:35906865:A:T	donor_gain	0.6100
9:35906304:G:GT	donor_gain	0.6000
9:35906490:G:GT	donor_gain	0.6000
9:35906539:T:G	donor_gain	0.6000
9:35906532:TGCCG:T	donor_gain	0.5900
9:35906858:G:T	donor_gain	0.5900
9:35906245:GA:G	donor_gain	0.5800
9:35906490:G:T	donor_gain	0.5800
9:35906823:G:GT	donor_gain	0.5800
9:35906841:A:AG	donor_gain	0.5800

AlphaMissense

741 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:35906333:G:C	G16R	0.860
9:35906346:C:A	A20E	0.825
9:35906334:G:A	G16D	0.806
9:35906340:C:A	A18D	0.793
9:35906321:G:A	G12R	0.782
9:35906321:G:C	G12R	0.782
9:35906384:T:C	F33L	0.771
9:35906386:C:A	F33L	0.771
9:35906386:C:G	F33L	0.771
9:35906352:T:G	L22R	0.767
9:35906378:T:C	C31R	0.754
9:35906358:T:G	L24R	0.751
9:35906412:A:T	E42V	0.749
9:35906349:T:A	V21D	0.748
9:35906355:T:G	L23R	0.739
9:35906306:A:C	S7R	0.734
9:35906308:C:A	S7R	0.734
9:35906308:C:G	S7R	0.734
9:35906324:T:A	W13R	0.725
9:35906324:T:C	W13R	0.725
9:35906419:C:A	N44K	0.708
9:35906419:C:G	N44K	0.708
9:35906406:A:T	D40V	0.695
9:35906407:C:A	D40E	0.676
9:35906407:C:G	D40E	0.676
9:35906322:G:A	G12E	0.670
9:35906468:T:C	F61L	0.669
9:35906470:C:A	F61L	0.669
9:35906470:C:G	F61L	0.669
9:35906352:T:A	L22Q	0.653

dbSNP variants (sampled 300 via entrez): RS1000029006 (9:35905823 A>G), RS1000626569 (9:35904501 C>T), RS1000831865 (9:35904793 T>C), RS1001375806 (9:35904524 C>T), RS1001478028 (9:35904697 C>G), RS1001667580 (9:35904631 C>T), RS1002525562 (9:35907585 G>A,C), RS1004532800 (9:35905247 C>G), RS1005870394 (9:35904486 G>C), RS1007881697 (9:35906737 G>A,C), RS1009178671 (9:35905360 A>C), RS1009771043 (9:35904240 C>A,T), RS1010054046 (9:35904662 G>C,T), RS1010131162 (9:35904477 G>A), RS1011173147 (9:35907101 G>A,C,T)

Disease associations

OMIM: gene MIM:621339 | disease phenotypes: MIM:607095

GenCC curated gene-disease

Mondo (1): anauxetic dysplasia (MONDO:0011773)

Orphanet (1): Anauxetic dysplasia (Orphanet:93347)

HPO phenotypes

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

GWAS associations

40 associations (top):

Study	Trait	p-value
GCST003818_81	Resting heart rate	1.000000e-08
GCST006227_8	Diastolic blood pressure	7.000000e-10
GCST009936_17	Venous thromboembolism	9.000000e-06
GCST010796_605	Electrocardiogram morphology (amplitude at temporal datapoints)	5.000000e-13
GCST010796_606	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-08
GCST010796_607	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-09
GCST010796_608	Electrocardiogram morphology (amplitude at temporal datapoints)	6.000000e-09
GCST010796_609	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-08
GCST010796_610	Electrocardiogram morphology (amplitude at temporal datapoints)	5.000000e-08
GCST010796_611	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-08
GCST010796_612	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-09
GCST010796_613	Electrocardiogram morphology (amplitude at temporal datapoints)	6.000000e-11
GCST010796_614	Electrocardiogram morphology (amplitude at temporal datapoints)	7.000000e-10
GCST010796_615	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-09
GCST010796_616	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-09
GCST010796_617	Electrocardiogram morphology (amplitude at temporal datapoints)	8.000000e-12
GCST010796_618	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-11
GCST010796_619	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-09
GCST010796_620	Electrocardiogram morphology (amplitude at temporal datapoints)	5.000000e-10
GCST010796_621	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-10
GCST010796_622	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-10
GCST010796_623	Electrocardiogram morphology (amplitude at temporal datapoints)	9.000000e-11
GCST010796_624	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-11
GCST010796_625	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-11
GCST010796_676	Electrocardiogram morphology (amplitude at temporal datapoints)	8.000000e-11
GCST010796_677	Electrocardiogram morphology (amplitude at temporal datapoints)	7.000000e-10
GCST010796_678	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-09
GCST010796_679	Electrocardiogram morphology (amplitude at temporal datapoints)	6.000000e-10
GCST010796_680	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-11
GCST010796_681	Electrocardiogram morphology (amplitude at temporal datapoints)	8.000000e-10

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure
EFO:0004327	electrocardiography
EFO:0008039	BMI-adjusted hip circumference

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C538256	Anauxetic dysplasia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	decreases expression, increases abundance	2
Calcitriol	increases expression, affects cotreatment	2
Particulate Matter	decreases expression, increases abundance	2
bisphenol A	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
pentanal	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
abrine	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	increases expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	increases expression	1
Cadmium	decreases expression, increases abundance	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Nickel	decreases expression	1
Silicon Dioxide	decreases expression	1
Testosterone	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	increases expression	1
Cadmium Chloride	increases abundance, decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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