R3HCC1L

Summary

R3HCC1L (R3H domain and coiled-coil containing 1 like, HGNC:23512) is a protein-coding gene on chromosome 10q24.2, encoding Coiled-coil domain-containing protein R3HCC1L (Q7Z5L2).

Located in exon-exon junction complex.

Source: NCBI Gene 27291 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 154 total
• MANE Select transcript: NM_001351015

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23512
Approved symbol	R3HCC1L
Name	R3H domain and coiled-coil containing 1 like
Location	10q24.2
Locus type	gene with protein product
Status	Approved
Aliases	GIDRP88, PSORT
Ensembl gene	ENSG00000166024
Ensembl biotype	protein_coding
Entrez	27291

Gene structure

Transcript identifiers

Ensembl transcripts: 42 — 42 protein_coding

ENST00000298999, ENST00000314594, ENST00000370584, ENST00000370586, ENST00000612478, ENST00000613938, ENST00000903208, ENST00000903209, ENST00000903210, ENST00000903211, ENST00000903212, ENST00000903213, ENST00000903214, ENST00000903215, ENST00000903216, ENST00000903217, ENST00000903218, ENST00000903219, ENST00000903220, ENST00000903221, ENST00000903222, ENST00000903223, ENST00000903224, ENST00000903225, ENST00000903226, ENST00000903227, ENST00000924825, ENST00000924826, ENST00000924827, ENST00000924828, ENST00000924829, ENST00000924830, ENST00000924831, ENST00000963058, ENST00000963059, ENST00000963060, ENST00000963061, ENST00000963062, ENST00000963063, ENST00000963064, ENST00000963065, ENST00000963066

RefSeq mRNA: 13 — MANE Select: NM_001351015 NM_001256619, NM_001256620, NM_001256621, NM_001351010, NM_001351011, NM_001351012, NM_001351013, NM_001351014, NM_001351015, NM_001351016, NM_001351017, NM_014472, NM_138469

CCDS: CCDS31267, CCDS58093, CCDS73178

Canonical transcript exons

ENST00000298999 — 10 exons

Exon	Start	End
ENSE00001099059	98236024	98236164
ENSE00001099060	98234446	98234516
ENSE00001099061	98235425	98235520
ENSE00001099063	98231512	98231687
ENSE00001453088	98244091	98244897
ENSE00001453092	98156093	98156147
ENSE00001453093	98134657	98134706
ENSE00002497545	98162883	98162975
ENSE00003537783	98163293	98163397
ENSE00003728851	98208101	98209899

Expression profiles

Bgee: expression breadth ubiquitous, 197 present calls, max score 93.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.0808 / max 162.6621, expressed in 1741 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
106478	10.6925	1737
106477	0.3883	208

Top tissues by expression

275 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	93.29	gold quality
right testis	UBERON:0004534	89.98	gold quality
left testis	UBERON:0004533	89.97	gold quality
sperm	CL:0000019	89.10	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.50	gold quality
testis	UBERON:0000473	88.18	gold quality
granulocyte	CL:0000094	87.00	gold quality
mucosa of transverse colon	UBERON:0004991	86.76	gold quality
lower esophagus mucosa	UBERON:0035834	86.31	gold quality
male germ cell	CL:0000015	85.75	silver quality
calcaneal tendon	UBERON:0003701	85.48	gold quality
skin of leg	UBERON:0001511	83.86	gold quality
ventricular zone	UBERON:0003053	83.73	gold quality
endocervix	UBERON:0000458	82.73	gold quality
ectocervix	UBERON:0012249	82.69	gold quality
transverse colon	UBERON:0001157	82.65	gold quality
tibial nerve	UBERON:0001323	82.61	gold quality
blood	UBERON:0000178	82.38	gold quality
skin of abdomen	UBERON:0001416	82.37	gold quality
cortical plate	UBERON:0005343	82.31	gold quality
small intestine Peyer’s patch	UBERON:0003454	82.02	gold quality
minor salivary gland	UBERON:0001830	81.91	gold quality
esophagus mucosa	UBERON:0002469	81.89	gold quality
spleen	UBERON:0002106	81.80	gold quality
muscle layer of sigmoid colon	UBERON:0035805	81.76	gold quality
popliteal artery	UBERON:0002250	81.70	gold quality
tibial artery	UBERON:0007610	81.70	gold quality
right lung	UBERON:0002167	81.62	gold quality
rectum	UBERON:0001052	81.53	gold quality
monocyte	CL:0000576	81.50	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

35 targeting R3HCC1L, 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-4673	100.00	66.64	1490
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-2116-3P	99.74	64.32	889
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-4666B	99.64	68.69	1282
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-642A-5P	99.51	65.10	1152
HSA-MIR-302B-5P	99.50	69.49	1857
HSA-MIR-302D-5P	99.50	69.34	1863
HSA-MIR-217-5P	99.49	69.93	1419
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-20A-3P	99.44	69.10	1575
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-4480	99.42	66.02	735
HSA-MIR-532-3P	99.34	65.76	1195
HSA-MIR-6807-3P	99.15	69.23	1275
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-5001-3P	98.91	67.28	1394
HSA-MIR-26B-3P	98.71	67.49	1102
HSA-MIR-6868-3P	98.63	69.64	2259
HSA-MIR-299-5P	98.56	71.14	1140
HSA-MIR-188-5P	97.89	67.01	756
HSA-MIR-4294	97.86	65.72	1110
HSA-MIR-3198	97.84	65.64	579
HSA-MIR-4309	97.84	65.45	588
HSA-MIR-6866-3P	97.38	66.94	748

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	r3hcc1l	ENSDARG00000089243
mus_musculus	R3hcc1l	ENSMUSG00000025184
rattus_norvegicus	R3hcc1l	ENSRNOG00000051256
drosophila_melanogaster	CG2162	FBGN0035388
caenorhabditis_elegans		WBGENE00008622

Paralogs (1): R3HCC1 (ENSG00000104679)

Protein

Protein identifiers

Coiled-coil domain-containing protein R3HCC1L — Q7Z5L2 (reviewed: Q7Z5L2)

Alternative names: Growth inhibition and differentiation-related protein 88, Putative mitochondrial space protein 32.1, R3H and coiled-coil domain-containing protein 1-like

All UniProt accessions (2): A0A384DVK4, Q7Z5L2

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. May interact with the exon junction complex (EJC) composed at least of CASC3, EIF4A3, MAGOH and RBM8A.

Tissue specificity. Expressed in placenta.

Isoforms (3)

UniProt ID	Names	Canonical?
Q7Z5L2-1	1	yes
Q7Z5L2-2	2
Q7Z5L2-3	3

RefSeq proteins (13): NP_001243548, NP_001243549, NP_001243550, NP_001337939, NP_001337940, NP_001337941, NP_001337942, NP_001337943, NP_001337944, NP_001337945, NP_001337946, NP_055287, NP_612478 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR039884	R3HC1/R3HCL	Family

UniProt features (21 total): sequence variant 7, region of interest 4, splice variant 3, sequence conflict 2, modified residue 2, chain 1, mutagenesis site 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z5L2-F1	51.36	0.11

Functional residue map

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

Post-translational modifications (2): 688, 712

Mutagenesis-validated functional residues (1):

Position	Phenotype
14–20	loss of interaction with the ejc.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 78 (showing top): IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GTTAAAG_MIR302B, DARWICHE_PAPILLOMA_PROGRESSION_RISK, MORF_RAD51L3, ATGTTAA_MIR302C, MORF_PRKCA, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, ELK1_01, MORF_ATF2, MORF_BCL2L11, MYB_Q5_01, GOCC_EXON_EXON_JUNCTION_COMPLEX, SCGGAAGY_ELK1_02, MORF_IL16, MORF_DMPK

GO Biological Process (0):

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

GO Cellular Component (1): exon-exon junction complex (GO:0035145)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
nuclear protein-containing complex	1

Protein interactions and networks

STRING

594 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
R3HCC1L	P0DN79	P0DN79	844
R3HCC1L	H7C2H4	H7C2H4	844
R3HCC1L	TBL1X	O60907	609
R3HCC1L	PDX1	P52945	448
R3HCC1L	PHGDH	O43175	434
R3HCC1L	TMEM89	A2RUT3	336
R3HCC1L	CEP55	Q53EZ4	330
R3HCC1L	SLC36A4	Q6YBV0	322
R3HCC1L	HSPD1	P10809	322
R3HCC1L	PALM3	A6NDB9	317
R3HCC1L	HEMK1	Q9Y5R4	307
R3HCC1L	BBX	Q8WY36	297
R3HCC1L	PSAT1	Q9Y617	275
R3HCC1L	HSPE1	P61604	270
R3HCC1L	ZBTB25	P24278	268

IntAct

13 interactions, top by confidence:

A	B	Type	Score
R3HCC1L	DNAAF19	psi-mi:“MI:0915”(physical association)	0.560
DNAAF19	R3HCC1L	psi-mi:“MI:0915”(physical association)	0.560
R3HCC1L	EEF1G	psi-mi:“MI:0915”(physical association)	0.400
EGLN3	FAM168B	psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
CDKN3	CST8	psi-mi:“MI:0914”(association)	0.350
SARS1	R3HCC1L	psi-mi:“MI:0914”(association)	0.350
CEP19	NUDT19	psi-mi:“MI:2364”(proximity)	0.270
MKS1	GARRE1	psi-mi:“MI:2364”(proximity)	0.270
POC1A	CCDC66	psi-mi:“MI:2364”(proximity)	0.270
EZR	EEF2K	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (29): CCDC103 (Two-hybrid), R3HCC1L (Affinity Capture-RNA), PABPC1 (Affinity Capture-Western), MAGOH (Affinity Capture-Western), RBM8A (Affinity Capture-Western), R3HCC1L (Affinity Capture-MS), R3HCC1L (Affinity Capture-MS), R3HCC1L (Proximity Label-MS), R3HCC1L (Proximity Label-MS), R3HCC1L (Proximity Label-MS), R3HCC1L (Affinity Capture-MS), R3HCC1L (Affinity Capture-MS), R3HCC1L (Affinity Capture-MS), R3HCC1L (Affinity Capture-MS), R3HCC1L (Proximity Label-MS)

ESM2 similar proteins: A0JM80, A6H8Y1, A7MBJ2, D3ZF42, E9Q6J5, F4I700, F4J3S1, F4KCE9, F6QRE9, O04251, O82345, P23497, P46100, P48785, P48786, Q04996, Q05B65, Q0WTB8, Q13342, Q15361, Q32MZ4, Q3UZ39, Q3ZBR9, Q4QSC8, Q571C7, Q5H9K5, Q5RHP9, Q61687, Q66HF9, Q7YQM3, Q7YQM4, Q7Z5L2, Q8BJM3, Q8C4A5, Q8C9B9, Q8GZ87, Q8H991, Q8IW19, Q92576, Q940Y3

Diamond homologs: Q7Z5L2, Q8BJM3, Q8BSI6, Q9Y3T6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	129
Likely benign	13
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2147 predictions. Top by Δscore:

Variant	Effect	Δscore
10:98209896:AGAGG:A	donor_loss	1.0000
10:98209897:GAG:G	donor_gain	1.0000
10:98209899:GGT:G	donor_loss	1.0000
10:98209900:G:T	donor_loss	1.0000
10:98209901:T:A	donor_loss	1.0000
10:98231510:A:AG	acceptor_gain	1.0000
10:98231511:G:GG	acceptor_gain	1.0000
10:98231511:GTT:G	acceptor_gain	1.0000
10:98231511:GTTA:G	acceptor_gain	1.0000
10:98231511:GTTAT:G	acceptor_gain	1.0000
10:98231683:TATCA:T	donor_gain	1.0000
10:98231684:ATCA:A	donor_gain	1.0000
10:98231685:TCA:T	donor_gain	1.0000
10:98231685:TCAG:T	donor_loss	1.0000
10:98231686:CA:C	donor_gain	1.0000
10:98231687:AGT:A	donor_loss	1.0000
10:98231688:GTGA:G	donor_gain	1.0000
10:98231689:T:A	donor_loss	1.0000
10:98231691:AGTA:A	donor_loss	1.0000
10:98231692:G:GG	donor_gain	1.0000
10:98234444:A:AG	acceptor_gain	1.0000
10:98234445:G:GA	acceptor_gain	1.0000
10:98234445:GA:G	acceptor_gain	1.0000
10:98234445:GAAA:G	acceptor_gain	1.0000
10:98234512:TACAG:T	donor_loss	1.0000
10:98234513:ACAGG:A	donor_loss	1.0000
10:98234514:CAGG:C	donor_loss	1.0000
10:98234515:AG:A	donor_loss	1.0000
10:98234516:GGT:G	donor_loss	1.0000
10:98234517:G:A	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000001213 (10:98193440 A>G), RS1000003852 (10:98173885 G>A), RS1000076583 (10:98145191 G>A,T), RS1000092823 (10:98207182 C>G), RS1000104993 (10:98174551 A>G), RS1000131768 (10:98157683 C>CT), RS1000153292 (10:98217707 T>C), RS1000163322 (10:98229507 A>G), RS1000203279 (10:98163646 C>T), RS1000235123 (10:98243161 T>C), RS1000265987 (10:98205820 A>C,G), RS1000279444 (10:98167669 A>G), RS1000283156 (10:98239786 G>A), RS1000301865 (10:98190751 C>T), RS1000313832 (10:98192750 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

2 associations (top):

Study	Trait	p-value
GCST002740_37	Inflammatory skin disease	7.000000e-06
GCST008129_21	Body mass index	8.000000e-16

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
bufotalin	increases expression	1
sodium arsenite	increases expression	1
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
ICG 001	increases expression	1
MT19c compound	increases expression	1
Resveratrol	increases expression, affects cotreatment	1
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression	1
Caffeine	decreases phosphorylation	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Methapyrilene	decreases methylation	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Thiram	increases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases expression	1
Copper Sulfate	increases 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_1870	MEC-1	Cancer cell line	Male

Clinical trials (associated diseases)

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