AiPD: Autoinhibited Protein Database

Q9Y3E1

Gene name	HDGFL3
Protein name	Hepatoma-derived growth factor-related protein 3
Names	HRP-3, Hepatoma-derived growth factor 2, HDGF-2
Species	Homo sapiens (Human)
KEGG Pathway	hsa:50810
EC number
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

63-203 (Predicted disordered autoinhibitory region) PR

Target domain
Relief mechanism
Assay	cis-regPred

AID

63-203 (Predicted disordered autoinhibitory region)

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

No accessory elements

References

Yeon JH et al. (2016) "Systems-wide Identification of cis-Regulatory Elements in Proteins", Cell Systems, 2, 89-100

Autoinhibited structure

Activated structure

6 structures for Q9Y3E1

Entry ID	Method	Resolution	Chain	Position	Source
6IIP	X-ray	095 A	A/B	8-94	PDB
6IIQ	X-ray	185 A	A/B/C	1-99	PDB
6IIR	X-ray	220 A	A/B	1-99	PDB
6IIS	X-ray	236 A	A/B	1-99	PDB
6IIT	X-ray	210 A	A/B	1-99	PDB
AF-Q9Y3E1-F1	Predicted				AlphaFoldDB

117 variants for Q9Y3E1

Variant ID(s)	Position	Change	Description	Diseaes Association	Provenance
rs1453088922 CA393314427	2	A>S		No	ClinGen gnomAD
CA393314424 rs1395510807	2	A>V		No	ClinGen gnomAD
CA393314418 rs1463740501	3	R>L		No	ClinGen gnomAD
CA393314401 rs1373679790	6	P>L		No	ClinGen gnomAD
CA7703682 rs751477122	7	R>C		No	ClinGen ExAC gnomAD
rs764106646 CA7703681	7	R>P		No	ClinGen ExAC TOPMed gnomAD
CA393314389 rs1469972532	8	E>D		No	ClinGen TOPMed gnomAD
rs1231600119 CA393314388	9	Y>N		No	ClinGen gnomAD
rs1203349272 CA393314367	11	A>V		No	ClinGen TOPMed
rs1483427154 CA393314356	13	D>G		No	ClinGen TOPMed
CA393314313 rs1248880614	19	M>I		No	ClinGen gnomAD
rs910220280 CA273506615	21	G>C		No	ClinGen TOPMed
rs1418612575 CA393314280	24	H>P		No	ClinGen TOPMed
rs1416727025 CA393320809	34	E>A		No	ClinGen gnomAD
CA393320754 rs1179267703	42	N>K		No	ClinGen TOPMed
rs1449599571 CA393320740	44	Y>C		No	ClinGen gnomAD
rs1172332473 CA393320729	46	I>V		No	ClinGen gnomAD
rs1567170453	49	F>L	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA393320688 rs1384525474	51	T>I		No	ClinGen gnomAD
rs559173257 CA7703641	54	T>N		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
CA7703619 rs779885695	57	L>I		No	ClinGen ExAC gnomAD
TCGA novel	59	P>L	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1284242851 CA393319680	60	K>E		No	ClinGen gnomAD
CA7703618 rs757419110	64	P>T		No	ClinGen ExAC gnomAD
CA393319611 rs1375984187	65	Y>C		No	ClinGen TOPMed gnomAD
rs1375984187 CA393319609	65	Y>F		No	ClinGen TOPMed gnomAD
TCGA novel	70	D>H	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA393319544 rs1344276226	72	F>L		No	ClinGen gnomAD
CA393319537 rs1300709314	73	G>R		No	ClinGen gnomAD
rs758456840 CA7703615	78	R>Q		No	ClinGen ExAC gnomAD
rs1426059260 CA393319500	78	R>W		No	ClinGen TOPMed gnomAD
CA393319469 rs145113533	82	N>K		No	ClinGen ESP ExAC TOPMed gnomAD
rs373778313 CA7703613	83	E>K		No	ClinGen ESP ExAC gnomAD
rs1267088572 CA393319422	89	E>Q		No	ClinGen gnomAD
rs1201662800 CA393319414	90	N>D		No	ClinGen gnomAD
CA273512671 rs917961875	90	N>S		No	ClinGen Ensembl
rs1201662800 CA393319413	90	N>Y		No	ClinGen gnomAD
CA7703610 rs766698301	92	P>A		No	ClinGen ExAC gnomAD
TCGA novel	95	K>T	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA273512647 rs992291510	96	F>L		No	ClinGen TOPMed gnomAD
rs772870099 CA7703608	97	T>I		No	ClinGen ExAC TOPMed gnomAD
rs747659212 CA393319352	99	Y>*		No	ClinGen ExAC gnomAD
rs201298885 CA273512646	99	Y>C		No	ClinGen Ensembl
rs11546524 CA273512238	101	A>G		No	ClinGen Ensembl
CA393319092 rs11546524	101	A>V		No	ClinGen Ensembl
rs200230620 CA7703584	102	I>V		No	ClinGen ESP ExAC TOPMed gnomAD
rs1029857853 CA273512231	103	Q>R		No	ClinGen TOPMed
CA7703583 rs554837315	104	Q>K		No	ClinGen 1000Genomes ExAC gnomAD
CA7703582 rs762467126	105	Q>E		No	ClinGen ExAC gnomAD
CA7703581 rs775359190	105	Q>R		No	ClinGen ExAC gnomAD
CA273512189 rs994754800	106	S>R		No	ClinGen Ensembl
CA393319014 rs1304753878	107	S>C		No	ClinGen gnomAD
TCGA novel	107	S>F	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1170470520 CA393318878	114	G>S		No	ClinGen gnomAD
CA393318866 rs1408893011	115	G>R		No	ClinGen gnomAD
rs199682422 CA273512186	117	T>I		No	ClinGen Ensembl
CA393318763 rs1168390472	120	A>V		No	ClinGen gnomAD
CA7703579 rs769653213	121	S>G		No	ClinGen ExAC gnomAD
CA273512177 rs961091056	123	E>D		No	ClinGen TOPMed gnomAD
rs1464807803 CA393318686	124	E>G		No	ClinGen TOPMed
CA273512169 rs542804499	126	G>D		No	ClinGen gnomAD
CA7703578 rs745645445	127	D>G		No	ClinGen ExAC TOPMed gnomAD
rs1016644390 CA273512168	129	V>I		No	ClinGen gnomAD
CA393318563 rs1446796969	130	E>A		No	ClinGen TOPMed
TCGA novel	130	E>K	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA393318568 rs1201779251	130	E>Q		No	ClinGen gnomAD
rs1567168933 CA393318527	131	E>D		No	ClinGen Ensembl
rs1483356064 CA393318517	132	D>V		No	ClinGen gnomAD
rs1005142659 CA273512140	133	G>A		No	ClinGen TOPMed gnomAD
TCGA novel	133	G>E	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
TCGA novel CA393318498 rs1331098792	133	G>R	Variant assessed as Somatic; impact. [NCI-TCGA]	No	ClinGen TOPMed NCI-TCGA
CA273512130 rs147777221	134	K>Q		No	ClinGen ESP TOPMed
rs780899046 CA7703576	135	G>D		No	ClinGen ExAC TOPMed gnomAD
CA393318403 rs1298167820	138	K>R		No	ClinGen gnomAD
CA7703575 rs535249266	139	N>I		No	ClinGen 1000Genomes ExAC gnomAD
CA393318378 rs1380249447	140	E>K		No	ClinGen gnomAD
rs1314567198 CA393318366	140	E>V		No	ClinGen gnomAD
rs1396436479 CA393318312	143	G>V		No	ClinGen TOPMed gnomAD
CA7703574 rs748314372	146	R>L		No	ClinGen ExAC gnomAD
COSM1719039 CA273512096 rs748314372	146	R>Q	NS [Cosmic]	No	ClinGen cosmic curated ExAC gnomAD
CA273512073 rs370356351	150	Y>C		No	ClinGen ESP ExAC TOPMed gnomAD
rs1431630854 CA393318208	150	Y>H		No	ClinGen gnomAD
rs370356351 CA7703573	150	Y>S		No	ClinGen ESP ExAC TOPMed gnomAD
CA393318172 rs1185596503	152	S>L		No	ClinGen gnomAD
rs1163452027 CA393318167	153	K>E		No	ClinGen gnomAD
rs1225283916 CA393316857	158	Q>E		No	ClinGen TOPMed
rs1284607933 CA393316823	159	S>P		No	ClinGen TOPMed
COSM297235 rs781730104 CA7703547	160	R>Q	Variant assessed as Somatic; 0.0 impact. large_intestine [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated ExAC NCI-TCGA TOPMed gnomAD
rs781098686 CA273507669	160	R>W		No	ClinGen gnomAD
rs1383484540 CA393316778	161	K>Q		No	ClinGen gnomAD
rs1161793568 CA393316753	162	S>T		No	ClinGen gnomAD
CA273507665 rs868583090	164	G>V		No	ClinGen Ensembl
rs757571791 CA7703546	165	D>V		No	ClinGen ExAC TOPMed gnomAD
TCGA novel	169	K>Q	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1567167475 CA393316576	170	D>H		No	ClinGen Ensembl
CA393316548 rs1298106037	171	C>F		No	ClinGen TOPMed gnomAD
CA393316534 rs1476721760	172	K>R		No	ClinGen gnomAD
CA393316488 rs1440756170	174	E>K		No	ClinGen gnomAD
CA7703544 rs763707408	177	K>R		No	ClinGen ExAC gnomAD
rs917837315 CA273507619	179	S>R		No	ClinGen TOPMed
rs990706628 CA273507608	183	G>E		No	ClinGen TOPMed
COSM244873 rs1446324632 CA393316249	185	A>V	prostate [Cosmic]	No	ClinGen cosmic curated TOPMed gnomAD
CA7703542 rs188845179	186	G>D		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
CA393316218 rs188845179	186	G>V		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
CA393316205 rs1172051462	187	N>S		No	ClinGen TOPMed
rs981197648 CA273507553	188	D>N		No	ClinGen TOPMed gnomAD
CA7703540 rs759098896	189	T>A		No	ClinGen ExAC gnomAD
CA393316151 rs1347160614	189	T>I		No	ClinGen TOPMed gnomAD
CA393316152 rs1347160614	189	T>R		No	ClinGen TOPMed gnomAD
CA393316136 rs1333908919	190	R>S		No	ClinGen TOPMed
CA393316094 rs1275477672	193	T>A		No	ClinGen gnomAD
rs1444228562 CA393316083	193	T>I		No	ClinGen TOPMed
CA393316040 rs1226844496	196	L>M		No	ClinGen gnomAD
rs776381808 CA7703539	200	S>G		No	ClinGen ExAC gnomAD
CA393315959 rs1567167441	200	S>N		No	ClinGen Ensembl
CA393315914 rs1436275682	201	E>D		No	ClinGen gnomAD
rs766448688 CA7703538	202	G>R		No	ClinGen ExAC gnomAD

No associated diseases with Q9Y3E1

2 regional properties for Q9Y3E1

Type	Name	Position	InterPro Accession
domain	PWWP domain	5 - 86	IPR000313
domain	Lens epithelium-derived growth factor, integrase-binding domain	472 - 569	IPR021567

Functions

		Description
EC Number
Subcellular Localization	Nucleus
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category	No pathway information available

4 GO annotations of cellular component

Name	Definition
cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

5 GO annotations of molecular function

Name	Definition
double-stranded DNA binding	Binding to double-stranded DNA.
growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
microtubule binding	Binding to a microtubule, a filament composed of tubulin monomers.
transcription coregulator activity	A transcription regulator activity that modulates the transcription of specific gene sets via binding to a DNA-bound DNA-binding transcription factor, either on its own or as part of a complex. Coregulators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators.
tubulin binding	Binding to monomeric or multimeric forms of tubulin, including microtubules.

4 GO annotations of biological process

Name	Definition
microtubule polymerization	The addition of tubulin heterodimers to one or both ends of a microtubule.
negative regulation of microtubule depolymerization	Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol.
neuron projection development	The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
regulation of transcription by RNA polymerase II	Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II.

13 homologous proteins in AiPD

UniProt AC	Gene Name	Protein Name	Species	Evidence Code
Q8MJG1	PSIP1	PC4 and SFRS1-interacting protein	Bos taurus (Bovine)	PR
Q9XSK7	HDGF	Hepatoma-derived growth factor	Bos taurus (Bovine)	PR
Q66T72	PSIP1	PC4 and SFRS1-interacting protein	Felis catus (Cat) (Felis silvestris catus)	PR
Q5XXA9	PSIP1	Lens epithelium-derived growth factor	Gallus gallus (Chicken)	PR
P51858	HDGF	Hepatoma-derived growth factor	Homo sapiens (Human)	PR
O75475	PSIP1	PC4 and SFRS1-interacting protein	Homo sapiens (Human)	PR
Q7Z4V5	HDGFL2	Hepatoma-derived growth factor-related protein 2	Homo sapiens (Human)	PR
Q99JF8	Psip1	PC4 and SFRS1-interacting protein	Mus musculus (Mouse)	PR
P51859	Hdgf	Hepatoma-derived growth factor	Mus musculus (Mouse)	PR
Q9JMG7	Hdgfl3	Hepatoma-derived growth factor-related protein 3	Mus musculus (Mouse)	PR
Q812D1	Psip1	PC4 and SFRS1-interacting protein	Rattus norvegicus (Rat)	PR
Q8VHK7	Hdgf	Hepatoma-derived growth factor	Rattus norvegicus (Rat)	PR
Q923W4	Hdgfl3	Hepatoma-derived growth factor-related protein 3	Rattus norvegicus (Rat)	PR

10	20	30	40	50	60
MARPRPREYK	AGDLVFAKMK	GYPHWPARID	ELPEGAVKPP	ANKYPIFFFG	THETAFLGPK
70	80	90	100	110	120
DLFPYKEYKD	KFGKSNKRKG	FNEGLWEIEN	NPGVKFTGYQ	AIQQQSSSET	EGEGGNTADA
130	140	150	160	170	180
SSEEEGDRVE	EDGKGKRKNE	KAGSKRKKSY	TSKKSSKQSR	KSPGDEDDKD	CKEEENKSSS
190	200
EGGDAGNDTR	NTTSDLQKTS	EGT