RNF24

Summary

RNF24 (ring finger protein 24, HGNC:13779) is a protein-coding gene on chromosome 20p13, encoding RING finger protein 24 (Q9Y225). May play a role in TRPCs intracellular trafficking.

This gene encodes an integral membrane protein that contains a RING-type zinc finger. The encoded protein may interact with multiple transient receptor potential cation channel subfamily C (TRPC) proteins and regulate the trafficking and insertion of these proteins into the plasma membrane.

Source: NCBI Gene 11237 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 19 total
• MANE Select transcript: NM_001134337

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13779
Approved symbol	RNF24
Name	ring finger protein 24
Location	20p13
Locus type	gene with protein product
Status	Approved
Aliases	G1L
Ensembl gene	ENSG00000101236
Ensembl biotype	protein_coding
OMIM	612489
Entrez	11237

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000336095, ENST00000358395, ENST00000432261, ENST00000545616, ENST00000905730, ENST00000905731, ENST00000905732

RefSeq mRNA: 4 — MANE Select: NM_001134337 NM_001134337, NM_001134338, NM_001321749, NM_007219

CCDS: CCDS13074, CCDS46577

Canonical transcript exons

ENST00000358395 — 6 exons

Exon	Start	End
ENSE00000657937	3934994	3935073
ENSE00000657938	3945177	3945218
ENSE00000858891	3927311	3934201
ENSE00001108661	3948237	3948279
ENSE00001539003	4015437	4015558
ENSE00003661754	3963875	3964024

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 95.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.2090 / max 948.6384, expressed in 1813 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
186179	23.8703	1813
186178	0.3387	143

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	95.84	gold quality
blood	UBERON:0000178	94.71	gold quality
pericardium	UBERON:0002407	94.54	gold quality
cartilage tissue	UBERON:0002418	93.31	gold quality
nipple	UBERON:0002030	92.58	gold quality
oocyte	CL:0000023	92.55	gold quality
renal medulla	UBERON:0000362	90.91	gold quality
stromal cell of endometrium	CL:0002255	90.44	gold quality
trigeminal ganglion	UBERON:0001675	88.32	gold quality
endothelial cell	CL:0000115	88.08	silver quality
descending thoracic aorta	UBERON:0002345	87.90	gold quality
cortical plate	UBERON:0005343	87.46	gold quality
dorsal root ganglion	UBERON:0000044	87.42	gold quality
monocyte	CL:0000576	87.16	gold quality
corpus epididymis	UBERON:0004359	87.08	gold quality
mononuclear cell	CL:0000842	87.02	gold quality
leukocyte	CL:0000738	87.01	gold quality
bone marrow	UBERON:0002371	86.77	gold quality
ganglionic eminence	UBERON:0004023	86.36	gold quality
thoracic aorta	UBERON:0001515	86.34	gold quality
ascending aorta	UBERON:0001496	86.27	gold quality
trabecular bone tissue	UBERON:0002483	85.47	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	85.28	gold quality
parotid gland	UBERON:0001831	85.25	gold quality
parietal lobe	UBERON:0001872	84.73	gold quality
synovial joint	UBERON:0002217	84.69	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.47	gold quality
embryo	UBERON:0000922	84.46	gold quality
bone marrow cell	CL:0002092	84.41	gold quality
inferior vagus X ganglion	UBERON:0005363	84.40	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

282 targeting RNF24, 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-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-6891-5P	99.98	66.53	1372

Literature-anchored findings (GeneRIF, showing 1)

• Results indicate that RNF24 interacts with TRPC cation channels in the Golgi apparatus and affects TRPC intracellular trafficking without affecting their activity. (PMID:17850865)

Cross-species orthologs

10 orthologs

Organism	Symbol	Gene ID
danio_rerio	rnf24	ENSDARG00000036965
mus_musculus	Rnf24	ENSMUSG00000048911
rattus_norvegicus	Rnf24	ENSRNOG00000088070
caenorhabditis_elegans		WBGENE00015641
caenorhabditis_elegans		WBGENE00015642
caenorhabditis_elegans		WBGENE00015818
caenorhabditis_elegans		WBGENE00017589
caenorhabditis_elegans		WBGENE00020665
caenorhabditis_elegans		WBGENE00022262
caenorhabditis_elegans		WBGENE00022265

Paralogs (1): RNF122 (ENSG00000133874)

Protein

Protein identifiers

RING finger protein 24 — Q9Y225 (reviewed: Q9Y225)

All UniProt accessions (1): Q9Y225

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in TRPCs intracellular trafficking.

Subunit / interactions. Interacts with TRPC1, TRPC3, TRPC4, TRPC5, TRPC6 and TRPC7.

Subcellular location. Golgi apparatus membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y225-1	1	yes
Q9Y225-2	2

RefSeq proteins (4): NP_001127809, NP_001127810, NP_001308678, NP_009150 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001841	Znf_RING	Domain
IPR011016	Znf_RING-CH	Domain
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR048025	RNF24_RING-H2	Domain
IPR050731	HRD1_E3_ubiq-ligases	Family

Pfam: PF13639

UniProt features (12 total): strand 4, turn 2, chain 1, transmembrane region 1, helix 1, zinc finger region 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2EP4	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y225-F1	70.82	0.14

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 197 (showing top): TGCGCANK_UNKNOWN, ENK_UV_RESPONSE_KERATINOCYTE_UP, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, MORF_RAD51L3, SP1_Q2_01, MAHAJAN_RESPONSE_TO_IL1A_DN, MORF_CTSB, BLALOCK_ALZHEIMERS_DISEASE_UP, MORF_IL4, RIGGI_EWING_SARCOMA_PROGENITOR_DN, MORF_PRKCA, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN, SCHLOSSER_SERUM_RESPONSE_DN, BENPORATH_NOS_TARGETS, CAAGGAT_MIR362

GO Biological Process (0):

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
binding	1
cation binding	1
Golgi apparatus	1
bounding membrane of organelle	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

784 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RNF24	TRPC6	Q9Y210	855
RNF24	TRPC4	Q9UBN4	691
RNF24	TRPC5	Q9UL62	688
RNF24	TRPM2	O94759	650
RNF24	TRPC3	Q13507	637
RNF24	TRPC1	P48995	605
RNF24	PANK2	Q9BZ23	585
RNF24	PCED1A	Q9H1Q7	498
RNF24	RWDD1	Q9H446	492
RNF24	UBOX5	O94941	475
RNF24	CLRN3	Q8NCR9	474
RNF24	KCTD9	Q7L273	463
RNF24	ANK2	Q01484	457
RNF24	ANK3	Q12955	455
RNF24	ANK1	P16157	454

IntAct

4 interactions, top by confidence:

A	B	Type	Score
UQCRH	RNF24	psi-mi:“MI:0915”(physical association)	0.560
RNF24	UQCRH	psi-mi:“MI:0915”(physical association)	0.560
MFSD14A	FAM171A2	psi-mi:“MI:0914”(association)	0.350

BioGRID (22): RNF24 (Two-hybrid), RNF24 (PCA), RNF24 (Two-hybrid), RNF24 (Two-hybrid), ARMC1 (Two-hybrid), NKG7 (Two-hybrid), TIMMDC1 (Two-hybrid), PLP1 (Two-hybrid), NT5E (Two-hybrid), VAMP1 (Two-hybrid), SLC10A6 (Two-hybrid), HIATL1 (Two-hybrid), NRSN1 (Two-hybrid), GOLT1A (Two-hybrid), BNIP3 (Two-hybrid)

ESM2 similar proteins: A0PJ23, A9JR22, A9JR44, B0BLK0, B0BLK7, B0BLK9, B2C4J2, B2MW50, B2ZDY1, E0VIU9, G1TZ76, J7H5K9, O43034, O64650, O73557, P03128, P11302, P11331, P18541, P19325, P19326, P36113, P42677, P47904, Q06651, Q06834, Q197D3, Q27YE2, Q27YE6, Q2KHT7, Q6IUF9, Q6IVU5, Q6R7D2, Q6R7D3, Q6RSS3, Q6UY71, Q6ZWU9, Q71TY3, Q7JUR5, Q7PN68

Diamond homologs: O13959, P62877, P62878, Q08273, Q20052, Q23457, Q3ZCF6, Q54K33, Q54L48, Q5R8A2, Q5UQ40, Q7X843, Q8BGI1, Q8QG64, Q940X7, Q9CPX9, Q9M2B0, Q9M9L0, Q9NHX0, Q9NYG5, Q9UBF6, Q9W5E1, Q9WTZ1, Q9Y225, A5WWA0, E9QAU8, F4HZZ4, F4HZZ5, O22197, O43567, O54965, O64763, P0C035, P0CH30, P0DPR2, P87119, Q06003, Q07G42, Q08CG8, Q08D68

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
Ub:E2	“up-regulates activity”	RNF24	ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1628 predictions. Top by Δscore:

Variant	Effect	Δscore
20:3934992:A:AC	donor_gain	1.0000
20:3934993:C:CA	donor_gain	1.0000
20:3934993:CTTT:C	donor_gain	1.0000
20:3935069:CAGAG:C	acceptor_gain	1.0000
20:3935074:C:CC	acceptor_gain	1.0000
20:3945171:ACTTA:A	donor_loss	1.0000
20:3945173:TTACC:T	donor_loss	1.0000
20:3945174:TA:T	donor_loss	1.0000
20:3945175:A:AG	donor_loss	1.0000
20:3945176:C:G	donor_loss	1.0000
20:3945217:ACCTG:A	donor_loss	1.0000
20:3964025:C:CC	acceptor_gain	1.0000
20:3934120:A:AC	donor_gain	0.9900
20:3934121:C:CC	donor_gain	0.9900
20:3934985:AATAC:A	donor_loss	0.9900
20:3934986:ATAC:A	donor_loss	0.9900
20:3934990:T:TG	donor_loss	0.9900
20:3934991:TACTT:T	donor_loss	0.9900
20:3934993:C:T	donor_loss	0.9900
20:3935071:GAG:G	acceptor_gain	0.9900
20:3935073:GC:G	acceptor_loss	0.9900
20:3935074:C:CA	acceptor_loss	0.9900
20:3945215:TAACC:T	donor_loss	0.9900
20:3945216:AACCT:A	acceptor_loss	0.9900
20:3945217:ACCT:A	acceptor_loss	0.9900
20:3945218:CCTG:C	acceptor_loss	0.9900
20:3945219:CTGTA:C	donor_loss	0.9900
20:3945220:T:TC	acceptor_loss	0.9900
20:3945220:TGTAA:T	donor_loss	0.9900
20:3945221:G:C	acceptor_loss	0.9900

AlphaMissense

983 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:3934156:G:C	C118W	1.000
20:3934157:C:A	C118F	1.000
20:3934157:C:G	C118S	1.000
20:3934157:C:T	C118Y	1.000
20:3934158:A:G	C118R	1.000
20:3934158:A:T	C118S	1.000
20:3934163:G:T	P116H	1.000
20:3934164:G:A	P116S	1.000
20:3934165:A:C	C115W	1.000
20:3934166:C:G	C115S	1.000
20:3934166:C:T	C115Y	1.000
20:3934167:A:G	C115R	1.000
20:3934167:A:T	C115S	1.000
20:3934184:A:G	L109P	1.000
20:3934186:C:A	W108C	1.000
20:3934186:C:G	W108C	1.000
20:3934187:C:G	W108S	1.000
20:3934188:A:G	W108R	1.000
20:3934188:A:T	W108R	1.000
20:3934196:A:G	L105P	1.000
20:3934196:A:T	L105H	1.000
20:3934198:G:C	C104W	1.000
20:3934199:C:G	C104S	1.000
20:3934200:A:G	C104R	1.000
20:3934200:A:T	C104S	1.000
20:3935001:G:C	H101D	1.000
20:3935002:G:C	F100L	1.000
20:3935002:G:T	F100L	1.000
20:3935003:A:C	F100C	1.000
20:3935003:A:G	F100S	1.000

dbSNP variants (sampled 300 via entrez): RS1000013313 (20:3997118 C>A,T), RS1000026891 (20:3945959 T>A), RS1000072371 (20:3989566 T>C), RS1000083616 (20:4001985 G>T), RS1000102545 (20:3942088 A>G), RS1000145218 (20:3927106 G>A), RS1000163399 (20:3964341 A>T), RS1000175950 (20:4008957 A>C), RS1000208689 (20:3969901 G>A), RS1000240591 (20:3960204 G>A), RS1000287047 (20:4015298 G>T), RS1000293108 (20:3960621 T>C), RS1000329289 (20:4015567 G>A), RS1000340368 (20:4015001 C>T), RS1000381913 (20:4015509 G>A,C)

Disease associations

OMIM: gene MIM:612489 | 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
GCST003803_5	Response to antidepressants in depression	2.000000e-06
GCST004114_1	Nevirapine-induced hypersensitivity in HIV (drug-induced liver injury)	6.000000e-07
GCST008839_433	Height	1.000000e-16
GCST010320_116	PR interval	2.000000e-15
GCST010321_92	PR interval	7.000000e-16
GCST010796_4419	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-08
GCST010796_4420	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-08
GCST011742_38	Triglyceride levels in HIV infection	9.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004462	PR interval
EFO:0004327	electrocardiography
EFO:0004530	triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

52 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression	4
bisphenol A	decreases methylation, increases expression	2
Air Pollutants	affects expression, increases abundance, increases expression	2
Formaldehyde	increases expression	2
bisphenol F	affects cotreatment, decreases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	increases expression	1
sodium arsenite	increases expression	1
benzo(e)pyrene	increases methylation	1
nickel sulfate	decreases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
oxamflatin	increases expression	1
apicidin	increases expression	1
K 7174	increases expression	1
scriptaid	increases expression	1
bisphenol S	increases methylation	1
Sunitinib	increases expression	1
Arsenic Trioxide	increases expression	1
Panobinostat	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	increases expression	1
Cisplatin	decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Deoxyglucose	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Diuron	decreases expression	1

Clinical trials (associated diseases)

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