Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	8820
Gene name	HESX homeobox 1
Gene symbol	HESX1
Synonyms (NCBI Gene)	ANFCPHD5RPX
Chromosome	3
Chromosome location	3p14.3
Summary	This gene encodes a conserved homeobox protein that is a transcriptional repressor in the developing forebrain and pituitary gland. Mutations in this gene are associated with septooptic dysplasia, HESX1-related growth hormone deficiency, and combined pitu

Show/Hide all (17)

SNP ID	Visualize variation	Clinical significance	Consequence
rs983243	A>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant, upstream transcript variant, genic upstream transcript variant
rs28936416	A>G	Pathogenic	Intron variant, missense variant, coding sequence variant
rs28936702	G>A	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs28936703	G>A	Uncertain-significance, pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs28936704	T>C	Uncertain-significance, pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs104893742	C>T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs121909173	C>G	Pathogenic	Missense variant, intron variant, coding sequence variant
rs141063672	C>T	Conflicting-interpretations-of-pathogenicity, benign	Synonymous variant, non coding transcript variant, coding sequence variant
rs575112817	A>G,T	Pathogenic	Splice donor variant, intron variant
rs587776664	GT>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs748460226	CT>-,CTCT	Pathogenic	Intron variant, coding sequence variant, frameshift variant
rs752434998	TG>-	Pathogenic, uncertain-significance	Non coding transcript variant, coding sequence variant, frameshift variant
rs754137696	A>C	Pathogenic	Coding sequence variant, intron variant, missense variant
rs777223697	A>T	Pathogenic, likely-pathogenic	Coding sequence variant, intron variant, stop gained
rs777833871	T>-	Pathogenic	Coding sequence variant, intron variant, frameshift variant
rs1238248024	C>A,G	Likely-pathogenic	Splice acceptor variant, intron variant
rs1286347776	CA>-	Likely-pathogenic	Coding sequence variant, intron variant, frameshift variant

Show/Hide all (2)

miRTarBase ID	miRNA	Experiments	Reference
MIRT024293	hsa-miR-215-5p	Microarray	19074876
MIRT026712	hsa-miR-192-5p	Microarray	19074876

Show/Hide all (1)

Transcription factor	Regulation	Reference
OTX2	Unknown	18628516

Show/Hide all (53)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IDA	11748154
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000785	Component	Chromatin	ISA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA	11748154
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA	26781211
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IMP	11748154
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IBA
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA	11748154
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA
GO:0003677	Function	DNA binding	IDA	26781211
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	TAS	9620767
GO:0003682	Function	Chromatin binding	IEA
GO:0005515	Function	Protein binding	IPI	23455924, 28514442, 32296183, 33961781
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	26781211
GO:0005634	Component	Nucleus	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007420	Process	Brain development	IEA
GO:0007420	Process	Brain development	TAS	9620767
GO:0008406	Process	Gonad development	IEA
GO:0010467	Process	Gene expression	IEA
GO:0016055	Process	Wnt signaling pathway	IEA
GO:0019827	Process	Stem cell population maintenance	IEA
GO:0021983	Process	Pituitary gland development	IBA
GO:0021983	Process	Pituitary gland development	IEA
GO:0021983	Process	Pituitary gland development	IEA
GO:0021983	Process	Pituitary gland development	IMP	26781211
GO:0030878	Process	Thyroid gland development	IEA
GO:0030900	Process	Forebrain development	IEA
GO:0030900	Process	Forebrain development	IEA
GO:0030916	Process	Otic vesicle formation	IEA
GO:0035264	Process	Multicellular organism growth	IEA
GO:0042803	Function	Protein homodimerization activity	IEA
GO:0043010	Process	Camera-type eye development	IEA
GO:0043565	Function	Sequence-specific DNA binding	IEA
GO:0043584	Process	Nose development	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	IEA
GO:0045995	Process	Regulation of embryonic development	IEA
GO:0048853	Process	Forebrain morphogenesis	IEA
GO:0048861	Process	Leukemia inhibitory factor signaling pathway	IEA
GO:0048863	Process	Stem cell differentiation	IEA
GO:0060070	Process	Canonical Wnt signaling pathway	IEA
GO:0070371	Process	ERK1 and ERK2 cascade	IEA
GO:0071276	Process	Cellular response to cadmium ion	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IEA

MIM	HGNC	e!Ensembl
601802	4877	ENSG00000163666

Q9UBX0

Protein name

Homeobox expressed in ES cells 1 (Homeobox protein ANF) (hAnf)

Protein function

Required for the normal development of the forebrain, eyes and other anterior structures such as the olfactory placodes and pituitary gland. Possible transcriptional repressor. Binds to the palindromic PIII sequence, 5'-AGCTTGAGTCTAATTGAATTAACTG

PDB

2K40

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00046	Homeodomain	109 → 165	Homeodomain	Domain

Sequence

MSPSLQEGAQLGENKPSTCSFSIERILGLDQKKDCVPLMKPHRPWADTCSSSGKDGNLCL
HVPNPPSGISFPSVVDHPMPEERASKYENYFSASERLSLKRELSWYRGRRPRTAFTQNQI
EVLENVFRVNCYPGIDIREDLAQKLNLEEDRIQIWFQNRRAKLKRSHRESQFLMAKKNFN
TNLLE

Sequence length

185

Interactions

View interactions

	KEGG
	Signaling pathways regulating pluripotency of stem cells

194

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
GROWTH HORMONE DEFICIENCY WITH PITUITARY ANOMALIES	Pathogenic; Likely pathogenic	rs2107565760, rs2060466023, rs748460226, rs2060462273, rs745873579, rs28936702, rs104893742, rs1238248024	RCV001973376 RCV001906782 RCV003073231 RCV002953019 RCV003021421 RCV005222672 RCV000008138 RCV000646790
Pituitary hormone deficiency, combined, 1	Likely pathogenic; Pathogenic	rs777223697, rs777833871	RCV000582144 RCV000583488
PITUITARY HORMONE DEFICIENCY, COMBINED, 5	Pathogenic	rs28936416, rs587776664, rs575112817	RCV000008134 RCV000008136 RCV000008137
Septo-optic dysplasia sequence	Pathogenic; Likely pathogenic	rs2107565760, rs2060466023, rs748460226, rs2060462273, rs745873579, rs28936702, rs2471733263, rs745685399, rs777223697, rs777833871, rs1238248024	RCV001973376 RCV001906782 RCV003073231 RCV002953019 RCV003021421 RCV000008130 RCV000008133 RCV000008135 RCV003153172 RCV000581553 RCV000582234 RCV000646790

Show/Hide Unknown Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Amenorrhea	Conflicting classifications of pathogenicity	rs143057250	RCV001849354
Colon adenocarcinoma	Benign	rs750212656	RCV005869940
Combined pituitary hormone deficiencies, genetic form	Conflicting classifications of pathogenicity	rs765353265	RCV005414283
Combined Pituitary Hormone Deficiency, Dominant/Recessive	Benign; Likely benign; Uncertain significance; Conflicting classifications of pathogenicity	rs9878928, rs886058753, rs148422263, rs886058754, rs549564119, rs886058755, rs983243	RCV000385780 RCV000294938 RCV000290957 RCV000306699 RCV000394503 RCV000302998 RCV000263151
HESX1-related disorder	Uncertain significance; Conflicting classifications of pathogenicity; Likely benign	rs761470587, rs770886420, rs28936703, rs143057250, rs778799278, rs528919258, rs754106154	RCV004753288 RCV004753369 RCV004752692 RCV003947822 RCV003402250 RCV003980956 RCV003974280
HESX1-Related Disorders	Conflicting classifications of pathogenicity	rs770886420	RCV004801040
Male infertility with spermatogenesis disorder	Conflicting classifications of pathogenicity	rs768165720	RCV003991580
SEPTOOPTIC DYSPLASIA, MILD	Uncertain significance	rs28936703	RCV000008131

Show/Hide Text Mining Associations (19)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adrenal Insufficiency	Associate	26781211
Alzheimer Disease	Associate	38527854
Capillary Malformation Arteriovenous Malformation	Associate	12372734
Chromosome Aberrations	Associate	34124982
Combined Pituitary Hormone Deficiency	Associate	14561704, 26781211, 27000987, 28332357, 32796691, 33451138
Dwarfism Pituitary	Associate	26781211, 27000987, 33451138
Hemochromatosis	Associate	27000987
Hereditary renal agenesis	Associate	27000987
Hypopituitarism	Associate	14561704, 27000987, 34124982
Hypothyroidism	Associate	26781211
Idiopathic Hypogonadotropic Hypogonadism	Associate	36700485
Kallmann Syndrome	Associate	23465708
Lewy Body Disease	Associate	38527854
Optic Atrophy	Associate	27343026
Osteoporosis	Associate	33451138
PEHO syndrome	Associate	27343026
Periventricular Nodular Heterotopia	Associate	12372734
Pituitary Diseases	Associate	12372734, 14561704, 18728160, 27000987, 34124982
Septo Optic Dysplasia	Associate	12372734, 14561704, 20949537, 26781211, 27000987, 28972157

HESX1 (HESX homeobox 1)