EDRF1

Summary

EDRF1 (erythroid differentiation regulatory factor 1, HGNC:24640) is a protein-coding gene on chromosome 10q26.2, encoding Erythroid differentiation-related factor 1 (Q3B7T1). Transcription factor involved in erythroid differentiation.

This gene may play a role in erythroid cell differentiation. The encoded protein inhibits DNA binding of the erythroid transcription factor GATA-1 and may regulate the expression of alpha-globin and gamma-globin. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 26098 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 107 total
• MANE Select transcript: NM_001202438

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24640
Approved symbol	EDRF1
Name	erythroid differentiation regulatory factor 1
Location	10q26.2
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp586F1019, FLJ21617
Ensembl gene	ENSG00000107938
Ensembl biotype	protein_coding
OMIM	620463
Entrez	26098

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 6 protein_coding, 5 retained_intron, 5 nonsense_mediated_decay

ENST00000337623, ENST00000356792, ENST00000368812, ENST00000368813, ENST00000368815, ENST00000419769, ENST00000469725, ENST00000481600, ENST00000525091, ENST00000525358, ENST00000525524, ENST00000527655, ENST00000530795, ENST00000885577, ENST00000930611, ENST00000965840

RefSeq mRNA: 2 — MANE Select: NM_001202438 NM_001202438, NM_015608

CCDS: CCDS55733, CCDS7646

Canonical transcript exons

ENST00000356792 — 25 exons

Exon	Start	End
ENSE00001418292	125763301	125764139
ENSE00001772128	125729003	125729104
ENSE00003458507	125729358	125729479
ENSE00003461963	125735644	125735904
ENSE00003474603	125737918	125737989
ENSE00003489913	125743058	125743276
ENSE00003494756	125733635	125733743
ENSE00003495995	125734072	125734183
ENSE00003503207	125725318	125725442
ENSE00003522878	125747863	125748012
ENSE00003525782	125725682	125725838
ENSE00003526001	125753694	125753845
ENSE00003533386	125723068	125723134
ENSE00003534362	125723811	125723936
ENSE00003539069	125747536	125747694
ENSE00003561834	125745707	125745930
ENSE00003575090	125730288	125730399
ENSE00003597103	125740463	125740651
ENSE00003597260	125733404	125733551
ENSE00003618749	125752799	125752914
ENSE00003625705	125738295	125738445
ENSE00003626737	125749412	125749565
ENSE00003671160	125721204	125721412
ENSE00003692845	125741001	125741201
ENSE00003843344	125719709	125719915

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 93.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.3581 / max 313.2340, expressed in 1807 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
107567	20.5796	1807
107568	0.7628	472
107566	0.0157	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	93.32	gold quality
tibia	UBERON:0000979	93.25	gold quality
left testis	UBERON:0004533	92.90	gold quality
secondary oocyte	CL:0000655	92.57	gold quality
oocyte	CL:0000023	92.22	gold quality
testis	UBERON:0000473	91.66	gold quality
body of pancreas	UBERON:0001150	91.24	gold quality
parotid gland	UBERON:0001831	91.22	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.46	gold quality
cerebellar hemisphere	UBERON:0002245	89.96	gold quality
cerebellar cortex	UBERON:0002129	89.88	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.75	gold quality
right ovary	UBERON:0002118	89.55	gold quality
epithelium of nasopharynx	UBERON:0001951	89.53	gold quality
left ovary	UBERON:0002119	89.52	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.18	gold quality
cerebellum	UBERON:0002037	88.94	gold quality
spleen	UBERON:0002106	88.85	gold quality
calcaneal tendon	UBERON:0003701	88.66	gold quality
endocervix	UBERON:0000458	88.48	gold quality
ventricular zone	UBERON:0003053	88.36	gold quality
tonsil	UBERON:0002372	88.33	gold quality
granulocyte	CL:0000094	87.95	gold quality
lymph node	UBERON:0000029	87.91	gold quality
ovary	UBERON:0000992	87.82	gold quality
body of uterus	UBERON:0009853	87.82	gold quality
small intestine Peyer’s patch	UBERON:0003454	87.79	gold quality
ectocervix	UBERON:0012249	87.66	gold quality
saliva-secreting gland	UBERON:0001044	87.64	gold quality
embryo	UBERON:0000922	87.59	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.93

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

46 targeting EDRF1, 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-5692A	100.00	74.40	6850
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-498-5P	99.76	69.64	1807
HSA-MIR-3617-5P	99.75	69.41	1968
HSA-MIR-641	99.75	69.35	1975
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4465	99.71	72.56	2096
HSA-MIR-6126	99.62	68.09	996
HSA-MIR-802	99.61	67.70	1254
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-203A-3P	99.49	70.56	2806
HSA-MIR-142-5P	99.48	70.92	2416
HSA-MIR-5590-3P	99.48	70.91	2429

Literature-anchored findings (GeneRIF, showing 1)

• EDRF1 regulated alpha- and gamma-globin gene synthesis by modulating DNA-binding activity of GATA-1 transcription factor. (PMID:12609092)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	edrf1	ENSDARG00000019834
mus_musculus	Edrf1	ENSMUSG00000039990
rattus_norvegicus	Edrf1	ENSRNOG00000017728
drosophila_melanogaster	CG6511	FBGN0035923

Protein

Protein identifiers

Erythroid differentiation-related factor 1 — Q3B7T1 (reviewed: Q3B7T1)

All UniProt accessions (5): Q3B7T1, E9PJ07, H0Y353, H0YCQ0, H0YCS2

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor involved in erythroid differentiation. Involved in transcriptional activation of the globin gene.

Subcellular location. Nucleus.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (4)

UniProt ID	Names	Canonical?
Q3B7T1-1	1	yes
Q3B7T1-3	2
Q3B7T1-4	3
Q3B7T1-5	4

RefSeq proteins (2): NP_001189367, NP_056423 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR056582	EDRF1_N	Domain
IPR056583	EDRF1_TPR	Domain

Pfam: PF23723, PF23788

UniProt features (19 total): splice variant 5, compositionally biased region 4, region of interest 4, repeat 2, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3B7T1-F1	76.41	0.38

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 84 (showing top): RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, MODULE_151, BROWNE_HCMV_INFECTION_12HR_UP, GTGCCTT_MIR506, GENTILE_UV_RESPONSE_CLUSTER_D2, GENTILE_UV_HIGH_DOSE_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, MODULE_114, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN, CHEN_HOXA5_TARGETS_9HR_UP, SCGGAAGY_ELK1_02, DAZARD_UV_RESPONSE_CLUSTER_G6, GEORGES_TARGETS_OF_MIR192_AND_MIR215, CDC5_01

GO Biological Process (1): positive regulation of DNA-templated transcription (GO:0045893)

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

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	1
regulation of DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

960 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EDRF1	HSPBP1	Q9NZL4	507
EDRF1	TEX36	Q5VZQ5	476
EDRF1	IGSF5	Q9NSI5	474
EDRF1	TMEM179	Q6ZVK1	453
EDRF1	GOLGA8J	A6NMD2	447
EDRF1	LARP1B	Q659C4	440
EDRF1	PDCD2L	Q9BRP1	430
EDRF1	KCNK5	O95279	393
EDRF1	PACC1	Q9H813	379
EDRF1	PPFIBP1	Q86W92	373
EDRF1	RNF41	Q9H4P4	363
EDRF1	ZNF454	Q8N9F8	358
EDRF1	ISCA1	Q9BUE6	355
EDRF1	HIKESHI	Q53FT3	350
EDRF1	PHF21B	Q96EK2	348

IntAct

157 interactions, top by confidence:

A	B	Type	Score
MED4	MED19	psi-mi:“MI:2364”(proximity)	0.900
HSP90AB1	HSP90AA1	psi-mi:“MI:0914”(association)	0.840
HSP90AA1	HSP90AB1	psi-mi:“MI:0914”(association)	0.840
CNOT11	CNOT1	psi-mi:“MI:0914”(association)	0.770
HSPA8	GAK	psi-mi:“MI:0914”(association)	0.760
SIL1	HSPA5	psi-mi:“MI:0914”(association)	0.740
TTC4	EDRF1	psi-mi:“MI:0914”(association)	0.730
HSP90AA1	CHUK	psi-mi:“MI:0914”(association)	0.670
HSP90AB1	CHUK	psi-mi:“MI:0914”(association)	0.670
AAGAB	AP2A2	psi-mi:“MI:0914”(association)	0.670
AIPL1	PDE5A	psi-mi:“MI:0914”(association)	0.640
LTO1	ABCE1	psi-mi:“MI:0914”(association)	0.640
EDRF1		psi-mi:“MI:0915”(physical association)	0.560
EDRF1	PHYH	psi-mi:“MI:0915”(physical association)	0.560
EDRF1	WFS1	psi-mi:“MI:0915”(physical association)	0.560
APP	EDRF1	psi-mi:“MI:0915”(physical association)	0.560
HTT	EDRF1	psi-mi:“MI:0915”(physical association)	0.560
ATXN3	EDRF1	psi-mi:“MI:0915”(physical association)	0.560
ATXN1	EDRF1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (138): EDRF1 (Two-hybrid), EDRF1 (Two-hybrid), SYCE1 (Two-hybrid), EDRF1 (Two-hybrid), EDRF1 (Affinity Capture-MS), EDRF1 (Affinity Capture-MS), EDRF1 (Affinity Capture-MS), EDRF1 (Affinity Capture-MS), EDRF1 (Affinity Capture-MS), EDRF1 (Affinity Capture-MS), EDRF1 (Affinity Capture-MS), EDRF1 (Affinity Capture-MS), EDRF1 (Affinity Capture-MS), EDRF1 (Proximity Label-MS), EDRF1 (Two-hybrid)

ESM2 similar proteins: A0A3Q2TTB3, A0JMR6, A4IIA7, F4JNY0, F6RRD7, I3XHK1, O60934, O88622, P14629, P28715, P79457, Q08DZ8, Q12789, Q17RS7, Q1LWH4, Q28I29, Q32PL8, Q3B7T1, Q4R7Q1, Q5FWP4, Q5M954, Q5QJC2, Q5RA37, Q5RCV3, Q5ZIN2, Q66J91, Q6GQV7, Q6NVF4, Q6P1E7, Q6P1H6, Q6P256, Q6P7W5, Q76CY8, Q7TP65, Q86W56, Q8BMI4, Q8C0W1, Q8C5W4, Q8GT06, Q8IXW5

Diamond homologs: Q3B7T1, Q5R9R1, Q6GQV7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 146 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Attenuation phase	5	21.9×	9e-04
Dengue Virus Genome Translation and Replication	5	17.1×	2e-03
HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand	8	16.6×	1e-05
Regulation of HSF1-mediated heat shock response	6	9.0×	7e-03

GO biological processes:

GO term	Partners	Fold	FDR
protein refolding	6	29.3×	2e-05
translational initiation	6	16.8×	5e-04
protein folding	13	10.5×	3e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	98
Likely benign	5
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

3772 predictions. Top by Δscore:

Variant	Effect	Δscore
10:125719913:CAGGT:C	donor_loss	1.0000
10:125719915:GGTG:G	donor_loss	1.0000
10:125719916:G:GG	donor_gain	1.0000
10:125721413:G:GA	donor_loss	1.0000
10:125721413:G:GG	donor_gain	1.0000
10:125721414:T:G	donor_loss	1.0000
10:125723062:T:TA	acceptor_gain	1.0000
10:125723063:G:A	acceptor_gain	1.0000
10:125723064:GTAGC:G	acceptor_loss	1.0000
10:125723066:A:AG	acceptor_gain	1.0000
10:125723066:AGC:A	acceptor_loss	1.0000
10:125723067:G:GA	acceptor_gain	1.0000
10:125723067:GC:G	acceptor_gain	1.0000
10:125723067:GCT:G	acceptor_gain	1.0000
10:125723067:GCTT:G	acceptor_gain	1.0000
10:125723067:GCTTT:G	acceptor_gain	1.0000
10:125723130:CTGAA:C	donor_gain	1.0000
10:125723131:TGAA:T	donor_gain	1.0000
10:125723131:TGAAG:T	donor_loss	1.0000
10:125723132:GAA:G	donor_gain	1.0000
10:125723132:GAAG:G	donor_gain	1.0000
10:125723132:GAAGT:G	donor_loss	1.0000
10:125723133:AA:A	donor_gain	1.0000
10:125723133:AAGTA:A	donor_loss	1.0000
10:125723134:AG:A	donor_loss	1.0000
10:125723135:G:GG	donor_gain	1.0000
10:125723136:TAAG:T	donor_loss	1.0000
10:125723800:A:AG	acceptor_gain	1.0000
10:125723806:TTAAG:T	acceptor_loss	1.0000
10:125723807:TAAG:T	acceptor_loss	1.0000

AlphaMissense

8201 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:125721333:T:A	W80R	1.000
10:125721333:T:C	W80R	1.000
10:125723819:A:C	K131N	1.000
10:125723819:A:T	K131N	1.000
10:125723824:T:C	L133P	1.000
10:125723827:T:C	L134P	1.000
10:125725430:T:C	F208S	1.000
10:125729391:T:A	W310R	1.000
10:125729391:T:C	W310R	1.000
10:125729437:T:A	I325K	1.000
10:125729437:T:G	I325R	1.000
10:125729439:T:C	F326L	1.000
10:125729441:T:A	F326L	1.000
10:125729441:T:G	F326L	1.000
10:125729464:T:A	V334D	1.000
10:125729466:A:C	S335R	1.000
10:125729468:C:A	S335R	1.000
10:125729468:C:G	S335R	1.000
10:125730319:G:A	G350R	1.000
10:125730319:G:C	G350R	1.000
10:125730320:G:A	G350E	1.000
10:125730326:A:T	D352V	1.000
10:125730331:T:A	W354R	1.000
10:125730331:T:C	W354R	1.000
10:125730335:T:C	L355S	1.000
10:125730337:G:C	D356H	1.000
10:125730338:A:C	D356A	1.000
10:125730338:A:T	D356V	1.000
10:125730342:C:A	N357K	1.000
10:125730342:C:G	N357K	1.000

dbSNP variants (sampled 300 via entrez): RS1000000908 (10:125752575 C>T), RS1000068356 (10:125760141 T>C), RS1000275734 (10:125733870 C>G,T), RS1000375607 (10:125720039 A>C,G), RS1000404225 (10:125726994 A>G), RS1000430964 (10:125727923 G>A,T), RS1000456697 (10:125759278 G>A), RS1000511762 (10:125759545 A>T), RS1000623327 (10:125732388 T>A,C), RS1000690102 (10:125734354 A>G), RS1000736586 (10:125725472 G>A,C), RS1000767024 (10:125721741 T>C), RS1000769080 (10:125726349 T>C), RS1000810912 (10:125752065 C>T), RS1000829607 (10:125720362 C>T)

Disease associations

OMIM: gene MIM:620463 | 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

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

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	decreases expression, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression, increases expression	2
daidzein	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
daidzin	affects cotreatment, increases expression	1
sodium arsenite	decreases expression, increases abundance	1
manganese chloride	decreases expression, increases abundance	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
genistin	affects cotreatment, increases expression	1
tamibarotene	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
glycitein	affects cotreatment, increases expression	1
2-palmitoylglycerol	increases expression	1
glycitin	affects cotreatment, increases expression	1
torcetrapib	increases expression	1
Resveratrol	increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	decreases expression	1
Acetaminophen	decreases expression	1
Acrolein	increases expression, increases abundance, affects cotreatment	1
Air Pollutants	affects cotreatment, increases abundance, increases expression	1
Arsenic	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Formaldehyde	decreases expression	1
Manganese	decreases expression, increases abundance	1
Ozone	increases abundance, affects cotreatment, increases expression	1
Tretinoin	decreases expression	1
Valproic Acid	decreases expression	1

Clinical trials (associated diseases)

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