RNF44

Summary

RNF44 (ring finger protein 44, HGNC:19180) is a protein-coding gene on chromosome 5q35.2, encoding RING finger protein 44 (Q7L0R7).

The protein encoded by this gene contains a RING finger, a motif present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions.

Source: NCBI Gene 22838 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 111 total
• MANE Select transcript: NM_014901

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19180
Approved symbol	RNF44
Name	ring finger protein 44
Location	5q35.2
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1100
Ensembl gene	ENSG00000146083
Ensembl biotype	protein_coding
OMIM	619283
Entrez	22838

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 13 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000274811, ENST00000504160, ENST00000504434, ENST00000506378, ENST00000508478, ENST00000509404, ENST00000513029, ENST00000515051, ENST00000904931, ENST00000904932, ENST00000904933, ENST00000904934, ENST00000904935, ENST00000904936, ENST00000904937, ENST00000939391, ENST00000939392, ENST00000939393, ENST00000939394

RefSeq mRNA: 1 — MANE Select: NM_014901 NM_014901

CCDS: CCDS4404

Canonical transcript exons

ENST00000274811 — 11 exons

Exon	Start	End
ENSE00001129097	176526712	176529090
ENSE00002051234	176530582	176530743
ENSE00003557838	176529288	176529387
ENSE00003624636	176529731	176529818
ENSE00003646036	176529523	176529644
ENSE00003648248	176530082	176530206
ENSE00004282466	176530848	176531021
ENSE00004282467	176532004	176532193
ENSE00004282468	176532366	176532516
ENSE00004282469	176531463	176531630
ENSE00004282470	176536940	176537402

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 97.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.6854 / max 470.9595, expressed in 1802 samples.

FANTOM5 promoters (16 alternative TSS)

Promoter ID	TPM avg	Samples expressed
65024	8.4616	1694
65021	5.8412	1324
65022	5.6409	1548
65015	2.4550	793
65026	2.1507	963
65017	1.9977	817
65020	1.8973	923
65019	1.6196	895
65016	1.1873	742
65018	1.1278	759

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	97.02	gold quality
thymus	UBERON:0002370	95.78	gold quality
spleen	UBERON:0002106	95.71	gold quality
lymph node	UBERON:0000029	94.68	gold quality
vermiform appendix	UBERON:0001154	94.27	gold quality
blood	UBERON:0000178	94.02	gold quality
right uterine tube	UBERON:0001302	93.68	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.36	gold quality
small intestine Peyer’s patch	UBERON:0003454	93.29	gold quality
postcentral gyrus	UBERON:0002581	93.07	gold quality
caecum	UBERON:0001153	93.04	gold quality
transverse colon	UBERON:0001157	92.98	gold quality
bone marrow cell	CL:0002092	92.97	gold quality
skin of abdomen	UBERON:0001416	92.86	gold quality
leukocyte	CL:0000738	92.83	gold quality
right lobe of thyroid gland	UBERON:0001119	92.62	gold quality
skin of leg	UBERON:0001511	92.56	gold quality
mononuclear cell	CL:0000842	92.52	gold quality
monocyte	CL:0000576	92.50	gold quality
left ovary	UBERON:0002119	92.48	gold quality
metanephros cortex	UBERON:0010533	92.44	gold quality
cerebellar cortex	UBERON:0002129	92.38	gold quality
cerebellar hemisphere	UBERON:0002245	92.38	gold quality
left lobe of thyroid gland	UBERON:0001120	92.37	gold quality
left testis	UBERON:0004533	92.32	gold quality
right ovary	UBERON:0002118	92.19	gold quality
right testis	UBERON:0004534	92.16	gold quality
parietal lobe	UBERON:0001872	92.10	gold quality
endometrium epithelium	UBERON:0004811	92.10	gold quality
minor salivary gland	UBERON:0001830	92.02	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-93593	yes	8.05
E-ANND-3	yes	4.77
E-ENAD-17	no	26.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

235 targeting RNF44, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-5692A	100.00	74.40	6850
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-6133	100.00	66.48	2064
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-59o9.10	ENSDARG00000089967
mus_musculus	Rnf44	ENSMUSG00000034928
rattus_norvegicus	Rnf44	ENSRNOG00000017641

Paralogs (3): RNF6 (ENSG00000127870), RLIM (ENSG00000131263), RNF38 (ENSG00000137075)

Protein

Protein identifiers

RING finger protein 44 — Q7L0R7 (reviewed: Q7L0R7)

All UniProt accessions (4): Q7L0R7, D6RAW5, D6RHW8, H0Y9W0

Isoforms (2)

UniProt ID	Names	Canonical?
Q7L0R7-1	1	yes
Q7L0R7-2	2

RefSeq proteins (1): NP_055716* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001841	Znf_RING	Domain
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily

Pfam: PF13639

UniProt features (5 total): chain 1, zinc finger region 1, region of interest 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7L0R7-F1	56.17	0.17

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 269 (showing top): ATF_B, GNF2_CASP8, TTTGTAG_MIR520D, MORF_SNRP70, MORF_HDAC1, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, MORF_HDAC2, CREB_Q4, MORF_TERF1, AGTCTTA_MIR499, YGACNNYACAR_UNKNOWN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, ATF1_Q6, GTGTTGA_MIR505, TGANTCA_AP1_C

GO Biological Process (1): protein ubiquitination (GO:0016567)

GO Molecular Function (4): zinc ion binding (GO:0008270), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein modification by small protein conjugation	1
transition metal ion binding	1
ubiquitin-protein transferase activity	1
ubiquitin-like protein ligase activity	1
binding	1
cation binding	1

Protein interactions and networks

STRING

790 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RNF44	NREP	Q16612	435
RNF44	LRRC23	Q53EV4	395
RNF44	DCAF12L2	Q5VW00	395
RNF44	RBM4B	Q9BQ04	383
RNF44	GLI4	P10075	379
RNF44	FAF2	Q96CS3	377
RNF44	ARL10	Q8N8L6	376
RNF44	ZNF512B	Q96KM6	370
RNF44	LYSMD1	Q96S90	370
RNF44	KCNQ5	Q9NR82	362
RNF44	PHRF1	Q9P1Y6	359
RNF44	SPG7	Q9UQ90	355
RNF44	PLP2	Q04941	349
RNF44	G5EA03	G5EA03	339
RNF44	PIN4	Q9Y237	339

IntAct

36 interactions, top by confidence:

A	B	Type	Score
RNF44	SPMIP9	psi-mi:“MI:0915”(physical association)	0.560
KRTAP19-5	RNF44	psi-mi:“MI:0915”(physical association)	0.560
RNF44	OXER1	psi-mi:“MI:0915”(physical association)	0.560
ARID5A	RNF44	psi-mi:“MI:0915”(physical association)	0.560
RNF44	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
	RNF44	psi-mi:“MI:0915”(physical association)	0.560
DAZAP2	RNF44	psi-mi:“MI:0915”(physical association)	0.560
RNF44	KRTAP19-1	psi-mi:“MI:0915”(physical association)	0.560
KRTAP21-2	RNF44	psi-mi:“MI:0915”(physical association)	0.560
KRTAP19-7	RNF44	psi-mi:“MI:0915”(physical association)	0.560
RNF44	BTNL3	psi-mi:“MI:0915”(physical association)	0.400
RNF44	SPMIP9	psi-mi:“MI:0915”(physical association)	0.000
RNF44	KRTAP19-5	psi-mi:“MI:0915”(physical association)	0.000
RNF44	OXER1	psi-mi:“MI:0915”(physical association)	0.000
RNF44	ARID5A	psi-mi:“MI:0915”(physical association)	0.000
RNF44	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.000
RNF44		psi-mi:“MI:0915”(physical association)	0.000
RNF44	DAZAP2	psi-mi:“MI:0915”(physical association)	0.000
RNF44	KRTAP19-1	psi-mi:“MI:0915”(physical association)	0.000
RNF44	KRTAP21-2	psi-mi:“MI:0915”(physical association)	0.000
RNF44	KRTAP19-7	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (18): RNF44 (Reconstituted Complex), RNF44 (Two-hybrid), OXER1 (Two-hybrid), TEX37 (Two-hybrid), DAZAP2 (Two-hybrid), KRTAP19-1 (Two-hybrid), KRTAP22-1 (Two-hybrid), KRTAP19-5 (Two-hybrid), KRTAP21-2 (Two-hybrid), ARID5A (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP19-7 (Two-hybrid), RNF44 (Affinity Capture-RNA), BTNL3 (Affinity Capture-MS), HIC2 (Affinity Capture-Western)

ESM2 similar proteins: A2AFE9, A2X0Q6, A3A2Z8, A5PJK7, B1ATL7, C7IW64, O65685, O94602, P03413, P11821, P38128, P80074, Q01196, Q03347, Q08775, Q0V9R0, Q10108, Q13761, Q2HRB6, Q5R476, Q5UQP5, Q63046, Q66J97, Q6AWY2, Q6F2E2, Q6NRV8, Q6PF39, Q6ZNA4, Q7L0R7, Q84JP1, Q8CFA7, Q8LFU0, Q8VY64, Q90ZT7, Q93ZH2, Q945M9, Q99ML9, Q9D1Z2, Q9E6P2, Q9FGD6

Diamond homologs: A5WWA0, E9QAU8, O22197, O43567, O49500, O54965, O64763, O80927, P0CH02, P0CH30, P0DPR2, Q06003, Q07G42, Q08CG8, Q08D68, Q0V9R0, Q0VD51, Q0WPW5, Q3T0W3, Q3U2C5, Q3UHJ8, Q4KLR8, Q4V7B8, Q566M8, Q5DTZ6, Q5M974, Q5NCP0, Q5R476, Q5RCV8, Q5SSZ7, Q5XIL0, Q641J8, Q66HG0, Q66J97, Q67YI6, Q68DV7, Q69U49, Q6AVN2, Q6AXU4, Q6GPV5

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
Ub:E2	“up-regulates activity”	RNF44	ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	88
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1668 predictions. Top by Δscore:

Variant	Effect	Δscore
5:176529289:TTCA:T	donor_gain	1.0000
5:176529515:GTACT:G	donor_loss	1.0000
5:176529516:TAC:T	donor_loss	1.0000
5:176529517:ACT:A	donor_loss	1.0000
5:176529518:CTC:C	donor_loss	1.0000
5:176529519:TCACA:T	donor_loss	1.0000
5:176529520:CA:C	donor_loss	1.0000
5:176529521:A:AC	donor_gain	1.0000
5:176529521:ACAG:A	donor_gain	1.0000
5:176529522:C:CA	donor_gain	1.0000
5:176529522:CA:C	donor_gain	1.0000
5:176529522:CAG:C	donor_gain	1.0000
5:176529522:CAGC:C	donor_gain	1.0000
5:176529522:CAGCG:C	donor_gain	1.0000
5:176529641:GGGC:G	acceptor_gain	1.0000
5:176529642:GGC:G	acceptor_gain	1.0000
5:176529643:GC:G	acceptor_gain	1.0000
5:176529644:CC:C	acceptor_gain	1.0000
5:176529645:C:CA	acceptor_loss	1.0000
5:176529645:C:CC	acceptor_gain	1.0000
5:176529646:T:A	acceptor_loss	1.0000
5:176529648:CA:C	acceptor_gain	1.0000
5:176529649:A:AC	acceptor_gain	1.0000
5:176529649:A:C	acceptor_gain	1.0000
5:176529732:T:TA	donor_gain	1.0000
5:176529814:TCGAG:T	acceptor_gain	1.0000
5:176529815:CGAG:C	acceptor_gain	1.0000
5:176529815:CGAGC:C	acceptor_gain	1.0000
5:176529816:GAG:G	acceptor_gain	1.0000
5:176529819:C:CC	acceptor_gain	1.0000

AlphaMissense

2777 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:176529065:C:G	R421P	1.000
5:176529067:G:C	C420W	1.000
5:176529068:C:A	C420F	1.000
5:176529068:C:G	C420S	1.000
5:176529068:C:T	C420Y	1.000
5:176529069:A:G	C420R	1.000
5:176529069:A:T	C420S	1.000
5:176529071:A:T	I419N	1.000
5:176529074:G:T	P418H	1.000
5:176529075:G:A	P418S	1.000
5:176529075:G:T	P418T	1.000
5:176529076:A:C	C417W	1.000
5:176529077:C:A	C417F	1.000
5:176529077:C:G	C417S	1.000
5:176529077:C:T	C417Y	1.000
5:176529078:A:C	C417G	1.000
5:176529078:A:G	C417R	1.000
5:176529078:A:T	C417S	1.000
5:176529292:A:G	L411S	1.000
5:176529294:C:A	W410C	1.000
5:176529294:C:G	W410C	1.000
5:176529295:C:G	W410S	1.000
5:176529296:A:G	W410R	1.000
5:176529296:A:T	W410R	1.000
5:176529304:A:T	V407D	1.000
5:176529306:A:C	C406W	1.000
5:176529307:C:A	C406F	1.000
5:176529307:C:G	C406S	1.000
5:176529307:C:T	C406Y	1.000
5:176529308:A:G	C406R	1.000

dbSNP variants (sampled 300 via entrez): RS1000124392 (5:176533143 A>C), RS1000407384 (5:176533377 T>C), RS1000653990 (5:176536777 TGGG>T,TGG,TGGGG,TGGGGG), RS1000654022 (5:176528718 C>T), RS1000885739 (5:176540623 C>T), RS1001070268 (5:176537902 G>A), RS1001107541 (5:176527169 A>C), RS1001254230 (5:176535805 C>T), RS1001297180 (5:176537166 C>A,T), RS1001716396 (5:176531278 C>G), RS1001739760 (5:176535656 C>G,T), RS1001926817 (5:176527730 G>A), RS1002245159 (5:176545200 C>G,T), RS1002340918 (5:176536810 C>A), RS1002354902 (5:176537054 C>T)

Disease associations

OMIM: gene MIM:619283 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001381_14	Menopause (age at onset)	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004704	age at menopause

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	4
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
Arsenic	decreases expression, increases abundance, increases expression, affects methylation, affects cotreatment	2
Cyclosporine	decreases expression, increases expression	2
GSK-J4	increases expression	1
dicrotophos	increases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
cobaltous chloride	increases expression	1
phenanthrene	decreases expression	1
beta-methylcholine	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
ICG 001	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	increases methylation	1
Vorinostat	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Atrazine	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Carbamazepine	affects expression	1
Cisplatin	decreases expression	1
Diazinon	increases methylation	1
Succimer	affects cotreatment, decreases expression	1
Diuron	decreases expression	1
Doxorubicin	decreases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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