ELF5

Summary

ELF5 (E74 like ETS transcription factor 5, HGNC:3320) is a protein-coding gene on chromosome 11p13, encoding ETS-related transcription factor Elf-5 (Q9UKW6). Transcriptionally activator that may play a role in regulating the later stages of keratinocytes terminal differentiation.

This gene encodes an epithelium-specific ETS family transcription factor. In addition to its role in regulating the later stages of terminal differentiation of keratinocytes, it appears to regulate a number of epithelium-specific genes found in tissues containing glandular epithelium such as salivary gland and prostate. It has very low affinity to DNA due to its negative regulatory domain at the amino terminus. This gene has been implicated as a tumor suppressive transcription factor in breast cancer.

Source: NCBI Gene 2001 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 44 total
• Transcription factor: yes — 11 downstream targets (CollecTRI)
• MANE Select transcript: NM_001422

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:3320
Approved symbol	ELF5
Name	E74 like ETS transcription factor 5
Location	11p13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000135374
Ensembl biotype	protein_coding
OMIM	605169
Entrez	2001

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 8 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000257832, ENST00000312319, ENST00000429939, ENST00000528709, ENST00000532417, ENST00000620316, ENST00000673820, ENST00000882062, ENST00000961186

RefSeq mRNA: 4 — MANE Select: NM_001422 NM_001243080, NM_001243081, NM_001422, NM_198381

CCDS: CCDS58129, CCDS73273, CCDS7892, CCDS7893

Canonical transcript exons

ENST00000257832 — 7 exons

Exon	Start	End
ENSE00000918380	34480772	34480967
ENSE00000918381	34482431	34482499
ENSE00000918383	34493479	34493712
ENSE00001185847	34513677	34513794
ENSE00002166521	34478791	34480314
ENSE00003558213	34490009	34490059
ENSE00003622071	34505629	34505753

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 98.74.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.2417 / max 367.1933, expressed in 158 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
119253	0.6878	118
119254	0.4654	61
119252	0.0644	10
119251	0.0241	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
parotid gland	UBERON:0001831	98.74	gold quality
amniotic fluid	UBERON:0000173	92.45	gold quality
saliva-secreting gland	UBERON:0001044	91.73	gold quality
seminal vesicle	UBERON:0000998	91.46	gold quality
epithelium of mammary gland	UBERON:0003244	91.04	gold quality
mammary duct	UBERON:0001765	90.26	gold quality
minor salivary gland	UBERON:0001830	90.00	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	88.99	gold quality
mucosa of paranasal sinus	UBERON:0005030	87.44	gold quality
mouth mucosa	UBERON:0003729	86.52	gold quality
nasal cavity mucosa	UBERON:0001826	86.00	gold quality
mammary gland	UBERON:0001911	84.60	gold quality
thoracic mammary gland	UBERON:0005200	84.44	gold quality
buccal mucosa cell	CL:0002336	82.43	gold quality
palpebral conjunctiva	UBERON:0001812	81.20	gold quality
renal medulla	UBERON:0000362	80.68	gold quality
trachea	UBERON:0003126	79.56	gold quality
metanephros cortex	UBERON:0010533	76.69	gold quality
lower lobe of lung	UBERON:0008949	75.81	silver quality
penis	UBERON:0000989	75.56	gold quality
tongue squamous epithelium	UBERON:0006919	75.50	gold quality
nasal cavity epithelium	UBERON:0005384	75.39	gold quality
skin of hip	UBERON:0001554	75.16	gold quality
skin of leg	UBERON:0001511	74.15	gold quality
bronchus	UBERON:0002185	73.72	gold quality
epithelium of bronchus	UBERON:0002031	73.71	gold quality
bronchial epithelial cell	CL:0002328	73.62	gold quality
mucosa of urinary bladder	UBERON:0001259	73.30	gold quality
sperm	CL:0000019	72.94	gold quality
skin of abdomen	UBERON:0001416	72.68	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-10855	yes	913.03
E-MTAB-6058	no	11.16
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

11 targets.

Target	Regulation
CCND2	Unknown
EGFR
FOLH1
FOXA1	Unknown
ITGB3
KLK3
KRT77
LARGE1
LYZ
MUC4
STAT5A

JASPAR motifs

Motif	Name	Family
MA0136.1	ELF5	Ets-related
MA0136.2	ELF5	Ets-related

JASPAR matrix evidence (PMIDs): PMID:16704374, PMID:20517297

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

81 targeting ELF5, 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-3613-3P	100.00	76.36	7965
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-148A-3P	99.74	73.77	1700
HSA-MIR-148B-3P	99.74	73.75	1700
HSA-MIR-152-3P	99.74	73.75	1703
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311

Literature-anchored findings (GeneRIF, showing 25)

• findings show that Ese-2 upregulates K18 gene expression through specific interactions within ETS binding sites in the regulatory first intron of the gene (PMID:15987600)
• Our studies have identified a critical stretch of nucleotides that is important for both basal as well as calcium responsive reporter activity and that binds to a nuclear factor, keratinocyte restricted factor (KRF). (PMID:16229011)
• Identification of the ESE-2 consensus site and characterization of the transcriptional activation properties of ESE-2 shed new light on its potential as a regulator of target genes. (PMID:16704374)
• ELF5 is expressed in the human placenta in villous cytotrophoblast cells but not in post-mitotic syncytiotrophoblast and invasive extravillous cytotrophoblast cells. (PMID:20354077)
• Loss of ELF5 is associated with kidney cancer. (PMID:21787113)
• Elf5 inhibits the epithelial-mesenchymal transition in mammary gland development and breast cancer metastasis by transcriptionally repressing Snail2. (PMID:23086238)
• ELF5 provides a key transcriptional determinant of breast cancer molecular subtype by suppression of estrogen sensitivity in luminal breast cancer cells. (PMID:23300383)
• we identified Elf5 as a novel biomarker of urothelial cancer on several biological levels and established a causative link between Elf5 and epithelial-mesenchymal transition in urothelial cancer. (PMID:25629735)
• The results of this study suggest that ELF5 is a candidate gene that confers genetic susceptibility for pediatric asthma in the Taiwanese population and SNP rs3910901 may have a minor impact on pediatric asthma in the Taiwanese population. (PMID:25648666)
• Elf5 expression is inversely correlated with epithelial-mesenchymal transition in prostate cancer. (PMID:25728398)
• Data (including data from studies in transgenic mice) suggest that expression of ELF5 in luminal breast cancer correlates with increased myeloid cell invasion, inflammation, and lung metastasis. (PMID:26717410)
• Alternative promoter use, conferring differential regulatory responses, is the main mechanism governing ELF5 action rather than differential transcriptional activity of the isoforms. (PMID:26738740)
• These results support the contention that ABO expression is dependent upon a downstream positive regulatory element functioning through a tissue-restricted transcription factor, Elf5, in epithelial cells. (PMID:27587399)
• a novel EWSR1/ETS chimeric gene, was identified in a patient diagnosed with refractory AML, suggesting a potential role of leukemogenesis in rare cases of AML. This fusion gene is very likely to exhibit oncogenic potential by interfering with the p53/p21-dependent pathway. (PMID:27627705)
• Low ELF5 expression is associated with ovarian cancer. (PMID:28184931)
• When ELF5 was transfected into the parental MCF7 cells that lack CEACAM1, lumen formation was restored, indicating that ELF5 can replace CEACAM1 in this model system of lumenogenesis. (PMID:28800960)
• Elf5 expression was associated with decreased overall and disease-free survival of triple negative breast cancers patients. (PMID:29396764)
• Authors found that expression of ELF5 was obviously decreased in ovarian cancer cell lines. The cells viability, invasion and metastasis were inhibited by overexpression ELF5. (PMID:30696803)
• Coordinate regulation of ELF5 and EHF at the chr11p13 CF modifier region. (PMID:31557407)
• ELF5 alters ER-driven gene expression via ER/FOXA1 cistrome and by modulating the expression of members of the ER transcriptional complex in breast cancer cells. (PMID:31895944)
• WWOX regulates the Elf5/Snail1 pathway to affect epithelial-mesenchymal transition of ovarian carcinoma cells in vitro. (PMID:32096174)
• A negative correlation between ELF5, FBXW7 and IFNGR1 expression in the tumours of patients with TNBC. (PMID:32284542)
• Breast-Specific Molecular Clocks Comprised of ELF5 Expression and Promoter Methylation Identify Individuals Susceptible to Cancer Initiation. (PMID:34140348)
• ELF5 inhibits the proliferation and invasion of breast cancer cells by regulating CD24. (PMID:34146197)
• ELF5 is a potential respiratory epithelial cell-specific risk gene for severe COVID-19. (PMID:35970849)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Elf5	ENSMUSG00000027186
rattus_norvegicus	Elf5	ENSRNOG00000008282

Paralogs (28): ETV1 (ENSG00000006468), ETV7 (ENSG00000010030), SPI1 (ENSG00000066336), ELF4 (ENSG00000102034), ETV2 (ENSG00000105672), ERF (ENSG00000105722), ELF2 (ENSG00000109381), ELK3 (ENSG00000111145), ETV3 (ENSG00000117036), ELF1 (ENSG00000120690), SPDEF (ENSG00000124664), ELK1 (ENSG00000126767), ETS1 (ENSG00000134954), EHF (ENSG00000135373), ETV6 (ENSG00000139083), FLI1 (ENSG00000151702), GABPA (ENSG00000154727), ERG (ENSG00000157554), ETS2 (ENSG00000157557), ELK4 (ENSG00000158711), ELF3 (ENSG00000163435), FEV (ENSG00000163497), SPIC (ENSG00000166211), ETV4 (ENSG00000175832), ETV5 (ENSG00000244405), ETV3L (ENSG00000253831), ERFL (ENSG00000268041), SPIB (ENSG00000269404)

Protein

Protein identifiers

ETS-related transcription factor Elf-5 — Q9UKW6 (reviewed: Q9UKW6)

Alternative names: E74-like factor 5, Epithelium-restricted ESE-1-related Ets factor, Epithelium-specific Ets transcription factor 2

All UniProt accessions (4): A0A087X1W9, A0A669KB78, A8K443, Q9UKW6

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptionally activator that may play a role in regulating the later stages of keratinocytes terminal differentiation. Isoform 2 binds to DNA sequences containing the consensus nucleotide core sequence GGA[AT]. Transcriptionally activates SPRR2A and the parotid gland-specific PSP promoters.

Subcellular location. Nucleus.

Tissue specificity. Expressed exclusively in tissues with a high content of epithelial cells. Highly expressed in salivary gland, mammary gland, kidney and prostate. Weakly expressed in placenta and lung. Isoform 1 and isoform 2 are differentially expressed in different tissues. In the kidney, only isoform 1 was expressed, while prostate expressed both isoforms, with levels of isoform 2 being higher. Expression is up-regulated during keratinocyte differentiation. Several epithelial carcinoma cell lines showed lack of expression.

Domain organisation. The PNT domain acts as a transcriptional activator.

Similarity. Belongs to the ETS family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9UKW6-1	1, ESE-2a	yes
Q9UKW6-2	2, ESE-2b
Q9UKW6-3	3
Q9UKW6-4	4

RefSeq proteins (4): NP_001230009, NP_001230010, NP_001413, NP_938195 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000418	Ets_dom	Domain
IPR003118	Pointed_dom	Domain
IPR013761	SAM/pointed_sf	Homologous_superfamily
IPR036388	WH-like_DNA-bd_sf	Homologous_superfamily
IPR036390	WH_DNA-bd_sf	Homologous_superfamily
IPR046328	ETS_fam	Family

Pfam: PF00178, PF02198

UniProt features (17 total): strand 4, splice variant 4, helix 3, turn 2, chain 1, domain 1, DNA-binding region 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
1WWX	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UKW6-F1	71.88	0.36

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-9927418	Developmental Lineage of Mammary Gland Luminal Epithelial Cells
R-HSA-9927426	Developmental Lineage of Mammary Gland Alveolar Cells

MSigDB gene sets: 158 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, YAATNRNNNYNATT_UNKNOWN, GOBP_SOMATIC_STEM_CELL_POPULATION_MAINTENANCE, GOBP_FORMATION_OF_PRIMARY_GERM_LAYER, GOZGIT_ESR1_TARGETS_DN, GOBP_MAMMARY_GLAND_EPITHELIUM_DEVELOPMENT, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_MAMMARY_GLAND_EPITHELIAL_CELL_DIFFERENTIATION, TCF4_Q5, GOBP_ECTODERM_DEVELOPMENT, GOBP_CELL_FATE_COMMITMENT_INVOLVED_IN_FORMATION_OF_PRIMARY_GERM_LAYER, MCBRYAN_PUBERTAL_BREAST_3_4WK_UP, TCF11_01, GOBP_GASTRULATION

GO Biological Process (10): ectodermal cell fate commitment (GO:0001712), regulation of transcription by RNA polymerase II (GO:0006357), cell differentiation (GO:0030154), somatic stem cell population maintenance (GO:0035019), mammary gland epithelial cell differentiation (GO:0060644), trophoblast giant cell differentiation (GO:0060707), negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806), regulation of DNA-templated transcription (GO:0006355), ectoderm development (GO:0007398), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (8): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Developmental Lineages of the Mammary Gland	2

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	2
cell differentiation involved in embryonic placenta development	2
regulation of transcription by RNA polymerase II	2
transcription cis-regulatory region binding	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
cellular anatomical structure	2
ectoderm formation	1
ectodermal cell differentiation	1
cell fate commitment involved in formation of primary germ layer	1
cellular developmental process	1
stem cell population maintenance	1
epithelial cell differentiation	1
mammary gland epithelium development	1
negative regulation of cell differentiation	1
regulation of cell differentiation involved in embryonic placenta development	1
negative regulation of reproductive process	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
tissue development	1
positive regulation of DNA-templated transcription	1
chromatin	1
DNA-binding transcription factor activity	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
transcription regulator activity	1
binding	1
DNA binding	1
chromosome	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1042 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ELF5	WFDC5	Q8TCV5	826
ELF5	CDX2	Q99626	787
ELF5	GATA3	P23771	753
ELF5	EOMES	O95936	747
ELF5	TEAD4	Q15561	734
ELF5	ITGB3	P05106	669
ELF5	GCM1	Q9NP62	604
ELF5	TFAP2C	Q92754	593
ELF5	CSN2	P05814	534
ELF5	FOXA1	P55317	527
ELF5	ESRRB	O95718	523
ELF5	PRLR	P16471	522
ELF5	SMAD3	P84022	501
ELF5	POU5F1	P31359	497
ELF5	PRL	P01236	497

IntAct

35 interactions, top by confidence:

A	B	Type	Score
GLRX2	ELF5	psi-mi:“MI:0915”(physical association)	0.560
ELF5	AKT1	psi-mi:“MI:2364”(proximity)	0.470
AKT1	ELF5	psi-mi:“MI:0915”(physical association)	0.470
ELF5	QDPR	psi-mi:“MI:0915”(physical association)	0.400
NFE2L2	ELF5	psi-mi:“MI:0915”(physical association)	0.370
ELF5	SS18L1	psi-mi:“MI:0915”(physical association)	0.370
ELF5	NFE2	psi-mi:“MI:0915”(physical association)	0.370
ELF5	ACTR2	psi-mi:“MI:0915”(physical association)	0.370
NRIP2	ELF5	psi-mi:“MI:0915”(physical association)	0.370
FRZB	ELF5	psi-mi:“MI:0915”(physical association)	0.370
ELF5	SIRT6	psi-mi:“MI:0915”(physical association)	0.370
ELF5	RPS15A	psi-mi:“MI:0915”(physical association)	0.370
ELF5	FLOT1	psi-mi:“MI:0914”(association)	0.350
ELF5	ARID1A	psi-mi:“MI:2364”(proximity)	0.270
FBXW7	ELF5	psi-mi:“MI:2364”(proximity)	0.270
SMAD4	ELF5	psi-mi:“MI:2364”(proximity)	0.270
SMARCA4	ELF5	psi-mi:“MI:2364”(proximity)	0.270
ELF5	SMARCA4	psi-mi:“MI:2364”(proximity)	0.270
SPOP	ELF5	psi-mi:“MI:2364”(proximity)	0.270
ELF5	SPOP	psi-mi:“MI:2364”(proximity)	0.270
EGFR	ELF5	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (54): SIRT6 (Two-hybrid), RPS15A (Two-hybrid), ELF5 (Two-hybrid), ELF5 (Two-hybrid), QDPR (Affinity Capture-MS), ELF5 (Affinity Capture-Western), EP300 (Affinity Capture-Western), SIRT6 (Affinity Capture-Western), ELF5 (Affinity Capture-Western), SIRT6 (Reconstituted Complex), ELF5 (Biochemical Activity), ELF5 (Affinity Capture-MS), ELF5 (Reconstituted Complex), NKX2-5 (Proximity Label-MS), ZNF281 (Proximity Label-MS)

ESM2 similar proteins: A0JMR6, A1A4L6, A1YG61, A2T737, O70273, O75747, P01105, P10157, P11308, P13474, P14921, P15036, P15037, P15062, P18755, P19102, P26323, P27577, P41156, P41157, P41212, P57782, P81270, P97360, Q08AW4, Q15052, Q32LN0, Q3SZL0, Q3US16, Q58DT0, Q60641, Q6GPJ8, Q6P3D7, Q7ZYI3, Q8BZ05, Q8C7R7, Q8HWS3, Q8N8B7, Q8NDB2, Q8VDK3

Diamond homologs: A0A1W2PQ73, A0JN51, A1A4L6, A1YF15, A1YG61, A1YG91, A2D4Z7, A2T737, A2T762, A3FEM2, A4GTP4, A8WFJ9, O00321, O01519, O70132, O70273, O95238, P01105, P10157, P11308, P11536, P13474, P14921, P15036, P15037, P15062, P18755, P18756, P19102, P19419, P20105, P26323, P27577, P28322, P28324, P29773, P29774, P29775, P29776, P32519

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

857 predictions. Top by Δscore:

Variant	Effect	Δscore
11:34480965:GGCC:G	acceptor_loss	1.0000
11:34480966:GCCT:G	acceptor_loss	1.0000
11:34480967:CCTT:C	acceptor_loss	1.0000
11:34480967:CCTTT:C	acceptor_gain	1.0000
11:34480968:C:CC	acceptor_gain	1.0000
11:34480968:CTTTT:C	acceptor_loss	1.0000
11:34480969:T:C	acceptor_gain	1.0000
11:34480969:T:G	acceptor_loss	1.0000
11:34480971:T:C	acceptor_gain	1.0000
11:34493474:CTGA:C	donor_loss	1.0000
11:34493475:TGACC:T	donor_loss	1.0000
11:34493476:GACC:G	donor_loss	1.0000
11:34493477:A:C	donor_loss	1.0000
11:34493709:CAGG:C	acceptor_gain	1.0000
11:34505625:GCAC:G	donor_loss	1.0000
11:34505626:CA:C	donor_loss	1.0000
11:34505627:A:C	donor_loss	1.0000
11:34505628:CCTGT:C	donor_gain	1.0000
11:34480963:GAGGC:G	acceptor_gain	0.9900
11:34480965:GGC:G	acceptor_gain	0.9900
11:34480966:GC:G	acceptor_gain	0.9900
11:34480968:C:T	acceptor_gain	0.9900
11:34480970:T:TC	acceptor_gain	0.9900
11:34480971:T:TC	acceptor_gain	0.9900
11:34482429:A:AC	donor_gain	0.9900
11:34482430:C:CC	donor_gain	0.9900
11:34482497:CATCT:C	acceptor_loss	0.9900
11:34482498:ATC:A	acceptor_loss	0.9900
11:34482499:TC:T	acceptor_loss	0.9900
11:34482500:CTGA:C	acceptor_loss	0.9900

AlphaMissense

1705 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:34480255:C:T	G254E	1.000
11:34480257:A:C	F253L	1.000
11:34480257:A:T	F253L	1.000
11:34480258:A:C	F253C	1.000
11:34480258:A:G	F253S	1.000
11:34480259:A:G	F253L	1.000
11:34480265:A:C	Y251D	1.000
11:34480265:A:G	Y251H	1.000
11:34480270:A:G	L249S	1.000
11:34480272:C:A	R248S	1.000
11:34480272:C:G	R248S	1.000
11:34480273:C:A	R248M	1.000
11:34480273:C:G	R248T	1.000
11:34480291:A:G	L242S	1.000
11:34480307:A:G	Y237H	1.000
11:34480314:T:A	R234S	1.000
11:34480314:T:G	R234S	1.000
11:34480772:C:A	R234I	1.000
11:34480772:C:G	R234T	1.000
11:34480773:T:C	R234G	1.000
11:34480775:A:G	L233P	1.000
11:34480778:G:T	A232D	1.000
11:34480779:C:G	A232P	1.000
11:34480780:T:A	R231S	1.000
11:34480780:T:G	R231S	1.000
11:34480781:C:A	R231I	1.000
11:34480781:C:G	R231T	1.000
11:34480782:T:C	R231G	1.000
11:34480783:G:C	S230R	1.000
11:34480783:G:T	S230R	1.000

dbSNP variants (sampled 300 via entrez): RS1000116542 (11:34487494 T>C), RS1000142518 (11:34498744 C>A), RS1000170726 (11:34484383 T>C), RS1000308751 (11:34513745 CCAG>C), RS1000354143 (11:34490243 G>A), RS1000384249 (11:34492985 G>A,T), RS1000425681 (11:34499039 C>T), RS1000446287 (11:34478348 G>A), RS1000455024 (11:34497044 A>G), RS1000536920 (11:34503592 G>A), RS1000760140 (11:34497485 T>G), RS1000768 (11:34492385 G>C,T), RS1000927163 (11:34514411 A>G), RS1000969741 (11:34481629 C>G), RS1000989819 (11:34495336 A>G)

Disease associations

OMIM: gene MIM:605169 | 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
GCST001800_1	β2-Glycoprotein I (β2-GPI) plasma levels	5.000000e-08
GCST009391_344	Metabolite levels	8.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004555	glycoprotein measurement
EFO:0010431	triacylglycerol 56:4 measurement

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
Valproic Acid	increases expression, affects cotreatment	4
trichostatin A	affects cotreatment, increases expression	3
mercuric bromide	increases expression, affects cotreatment	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases methylation, increases expression, affects expression	2
Panobinostat	affects cotreatment, increases expression	2
Estradiol	decreases expression, increases reaction, affects cotreatment, increases expression	2
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
sotorasib	affects cotreatment, increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
16 alpha-ethyl-21-hydroxy-19-nor-4-pregnene-3,20-dione	increases expression, increases response to substance, decreases reaction, affects binding, increases reaction	1
benzo(e)pyrene	decreases methylation	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
hydroquinone	increases expression	1
ciglitazone	affects binding, increases expression	1
CGP 52608	affects binding, increases reaction	1
dorsomorphin	increases expression, affects cotreatment	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	increases expression, increases response to substance	1
trametinib	affects cotreatment, increases expression	1
NVP-BKM120	affects cotreatment, increases expression	1
Air Pollutants	decreases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Coumestrol	decreases expression, affects cotreatment	1
Dexamethasone	affects cotreatment, decreases expression	1
Drugs, Chinese Herbal	increases expression	1
Folic Acid	decreases expression	1
Methapyrilene	decreases methylation	1
Naphthoquinones	increases expression	1
Promegestone	increases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, increases expression	1

Cellosaurus cell lines

5 cell lines: 5 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A1H8	SEES3-1V human ELF5, clone1	Embryonic stem cell	Male
CVCL_A1H9	SEES3-1V human ELF5, clone2	Embryonic stem cell	Male
CVCL_A1I0	SEES3-1V human ELF5, clone3	Embryonic stem cell	Male
CVCL_A1I1	SEES3-1V human ELF5, clone4	Embryonic stem cell	Male
CVCL_A1I2	SEES3-1V human ELF5, clone5	Embryonic stem cell	Male

Clinical trials (associated diseases)

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