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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	83932
Gene name Gene Name - the full gene name approved by the HGNC.	SprT-like N-terminal domain
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SPRTN
Synonyms (NCBI Gene) Gene synonyms aliases	C1orf124, DVC1, PRO4323, spartan
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1q42.2
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene may play a role in DNA repair during replication of damaged DNA. This protein recruits valosin containing protein (p97) to stalled DNA replication forks where it may prevent excessive translesional DNA synthesis and limit

Show/Hide all(3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs527236212	A>-	Pathogenic	Coding sequence variant, frameshift variant, 3 prime UTR variant
rs527236213	A>G	Pathogenic	Genic upstream transcript variant, upstream transcript variant, coding sequence variant, missense variant, intron variant
rs587593493	GGTA>-	Pathogenic	Coding sequence variant, frameshift variant, splice donor variant, intron variant

Show/Hide all(72)

miRTarBase ID	miRNA	Experiments	Reference
MIRT016242	hsa-miR-548b-3p	Sequencing	20371350
MIRT021124	hsa-miR-186-5p	Sequencing	20371350
MIRT045975	hsa-miR-125b-5p	CLASH	23622248
MIRT045716	hsa-miR-125a-5p	CLASH	23622248
MIRT713269	hsa-miR-512-5p	HITS-CLIP	19536157
MIRT713273	hsa-miR-548c-3p	HITS-CLIP	19536157
MIRT713272	hsa-miR-7151-5p	HITS-CLIP	19536157
MIRT713271	hsa-miR-3688-3p	HITS-CLIP	19536157
MIRT713270	hsa-miR-4261	HITS-CLIP	19536157
MIRT713269	hsa-miR-512-5p	HITS-CLIP	19536157
MIRT713268	hsa-miR-545-3p	HITS-CLIP	19536157
MIRT713267	hsa-miR-486-5p	HITS-CLIP	19536157
MIRT713266	hsa-miR-7152-5p	HITS-CLIP	19536157
MIRT565490	hsa-miR-124-3p	PAR-CLIP	20371350
MIRT565491	hsa-miR-506-3p	PAR-CLIP	20371350
MIRT565490	hsa-miR-124-3p	PAR-CLIP	20371350
MIRT565489	hsa-miR-3714	PAR-CLIP	20371350
MIRT565488	hsa-miR-3910	PAR-CLIP	20371350
MIRT565487	hsa-miR-5586-3p	PAR-CLIP	20371350
MIRT565486	hsa-miR-29a-3p	PAR-CLIP	20371350
MIRT565485	hsa-miR-29b-3p	PAR-CLIP	20371350
MIRT565484	hsa-miR-29c-3p	PAR-CLIP	20371350
MIRT565483	hsa-miR-6871-3p	PAR-CLIP	20371350
MIRT565482	hsa-miR-875-5p	PAR-CLIP	20371350
MIRT565481	hsa-miR-31-5p	PAR-CLIP	20371350
MIRT565480	hsa-miR-1257	PAR-CLIP	20371350
MIRT565479	hsa-miR-5682	PAR-CLIP	20371350
MIRT565478	hsa-miR-3144-3p	PAR-CLIP	20371350
MIRT560190	hsa-miR-1277-5p	PAR-CLIP	20371350
MIRT560189	hsa-miR-193a-3p	PAR-CLIP	20371350
MIRT560188	hsa-miR-193b-3p	PAR-CLIP	20371350
MIRT560187	hsa-miR-892b	PAR-CLIP	20371350
MIRT560186	hsa-miR-1278	PAR-CLIP	20371350
MIRT560185	hsa-miR-3128	PAR-CLIP	20371350
MIRT560184	hsa-miR-548ao-5p	PAR-CLIP	20371350
MIRT560183	hsa-miR-548ax	PAR-CLIP	20371350
MIRT560182	hsa-miR-5585-5p	PAR-CLIP	20371350
MIRT560181	hsa-miR-4470	PAR-CLIP	20371350
MIRT713269	hsa-miR-512-5p	HITS-CLIP	19536157
MIRT713273	hsa-miR-548c-3p	HITS-CLIP	19536157
MIRT713272	hsa-miR-7151-5p	HITS-CLIP	19536157
MIRT713271	hsa-miR-3688-3p	HITS-CLIP	19536157
MIRT713270	hsa-miR-4261	HITS-CLIP	19536157
MIRT713269	hsa-miR-512-5p	HITS-CLIP	19536157
MIRT713268	hsa-miR-545-3p	HITS-CLIP	19536157
MIRT713267	hsa-miR-486-5p	HITS-CLIP	19536157
MIRT713266	hsa-miR-7152-5p	HITS-CLIP	19536157
MIRT565490	hsa-miR-124-3p	PAR-CLIP	20371350
MIRT565491	hsa-miR-506-3p	PAR-CLIP	20371350
MIRT565490	hsa-miR-124-3p	PAR-CLIP	20371350
MIRT565489	hsa-miR-3714	PAR-CLIP	20371350
MIRT565488	hsa-miR-3910	PAR-CLIP	20371350
MIRT565487	hsa-miR-5586-3p	PAR-CLIP	20371350
MIRT565486	hsa-miR-29a-3p	PAR-CLIP	20371350
MIRT565485	hsa-miR-29b-3p	PAR-CLIP	20371350
MIRT565484	hsa-miR-29c-3p	PAR-CLIP	20371350
MIRT565483	hsa-miR-6871-3p	PAR-CLIP	20371350
MIRT565482	hsa-miR-875-5p	PAR-CLIP	20371350
MIRT565481	hsa-miR-31-5p	PAR-CLIP	20371350
MIRT565480	hsa-miR-1257	PAR-CLIP	20371350
MIRT565479	hsa-miR-5682	PAR-CLIP	20371350
MIRT565478	hsa-miR-3144-3p	PAR-CLIP	20371350
MIRT560190	hsa-miR-1277-5p	PAR-CLIP	20371350
MIRT560189	hsa-miR-193a-3p	PAR-CLIP	20371350
MIRT560188	hsa-miR-193b-3p	PAR-CLIP	20371350
MIRT560187	hsa-miR-892b	PAR-CLIP	20371350
MIRT560186	hsa-miR-1278	PAR-CLIP	20371350
MIRT560185	hsa-miR-3128	PAR-CLIP	20371350
MIRT560184	hsa-miR-548ao-5p	PAR-CLIP	20371350
MIRT560183	hsa-miR-548ax	PAR-CLIP	20371350
MIRT560182	hsa-miR-5585-5p	PAR-CLIP	20371350
MIRT560181	hsa-miR-4470	PAR-CLIP	20371350

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	IDA	27852435, 27871365, 27871366, 32649882
GO:0003690	Function	Double-stranded DNA binding	IDA	27852435, 27871365, 27871366, 32649882
GO:0003697	Function	Single-stranded DNA binding	IDA	27871365, 32649882
GO:0004222	Function	Metalloendopeptidase activity	IDA	27852435, 27871365, 27871366, 32649882
GO:0005515	Function	Protein binding	IPI	22681887, 22894931, 22902628, 23042605, 23042607
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005634	Component	Nucleus	IDA	22681887, 22894931, 23042605, 23042607, 27852435
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0006508	Process	Proteolysis	IDA	27852435, 27871365, 27871366, 32649882
GO:0006974	Process	Cellular response to DNA damage stimulus	IBA	21873635
GO:0006974	Process	Cellular response to DNA damage stimulus	IDA	22681887, 22894931, 22902628, 23042605, 23042607, 27852435, 27871365, 27871366, 32649882
GO:0009411	Process	Response to UV	IDA	22681887, 22894931, 22902628
GO:0016540	Process	Protein autoprocessing	IDA	27852435, 27871365, 27871366, 32649882
GO:0016607	Component	Nuclear speck	IDA
GO:0019985	Process	Translesion synthesis	IDA	22681887, 22902628
GO:0019985	Process	Translesion synthesis	IMP	23042605, 23042607
GO:0031398	Process	Positive regulation of protein ubiquitination	IDA	22681887
GO:0031593	Function	Polyubiquitin modification-dependent protein binding	IBA	21873635
GO:0043130	Function	Ubiquitin binding	IDA	22681887, 22894931, 22902628, 23042605, 23042607
GO:0046872	Function	Metal ion binding	IEA
GO:0070530	Function	K63-linked polyubiquitin modification-dependent protein binding	IDA	22681887, 23042605
GO:0070987	Process	Error-free translesion synthesis	TAS
GO:0106300	Process	Protein-DNA covalent cross-linking repair	IDA	27852435, 27871365, 27871366, 32152270, 32649882

MIM	HGNC	e!Ensembl
616086	25356	ENSG00000010072

Protein

UniProt ID

Q9H040

Protein name

DNA-dependent metalloprotease SPRTN (EC 3.4.24.-) (DNA damage protein targeting VCP) (DVC1) (Protein with SprT-like domain at the N terminus) (Spartan)

Protein function

DNA-dependent metalloendopeptidase that mediates the proteolytic cleavage of covalent DNA-protein cross-links (DPCs) during DNA synthesis, thereby playing a key role in maintaining genomic integrity (PubMed:27852435, PubMed:27871365, PubMed:2787

PDB

5IY4 , 6MDW , 6MDX

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF10263	SprT-like	45 → 153	SprT-like family	Domain

Sequence

MDDDLMLALRLQEEWNLQEAERDHAQESLSLVDASWELVDPTPDLQALFVQFNDQFFWGQ
LEAVEVKWSVRMTLCAGICSYEGKGGMCSIRLSEPLLKLRPRKDLVETLLHEMIHAYLFV
TNNDKDREGHGPEFCKHMHRINSLTGANITVYHTFHDEVDEYRRHWWRCNGPCQHRPPYY
GYVKRATNREPSAHDYWWAEHQKTCGGTYIKIKEPENYSKKGKGKAKLGKEPVLAAENKD
KPNRGEAQLVIPFSGKGYVLGETSNLPSPGKLITSHAINKTQDLLNQNHSANAVRPNSKI
KVKFEQNGSSKNSHLVSPAVSNSHQNVLSNYFPRVSFANQKAFRGVNGSPRISVTVGNIP
KNSVSSSSQRRVSSSKISLRNSSKVTESASVMPSQDVSGSEDTFPNKRPRLEDKTVFDNF
FIKKEQIKSSGNDPKYSTTTAQNSSSSSSQSKMVNCPVCQNEVLESQINEHLDWCLEGDS
IKVKSEESL

Sequence length

489

Interactions

View interactions

	Reactome
			Translesion Synthesis by POLH

Show/Hide Causal Diseases (3)

Disease term	Disease name	dbSNP ID
Causal
Cockayne syndrome	Cockayne Syndrome	rs121917900, rs121917901, rs121917902, rs387906262, rs2132552521, rs121917903, rs1590474873, rs121917904, rs121434323, rs121434324, rs121434325, rs121434326, rs121913028, rs185142838, rs527236039 View all (69 more)
Lipodystrophy	Lipodystrophy	rs553668, rs766817317
Progeroid features hepatocellular carcinoma predisposition syndrome	Progeroid features-hepatocellular carcinoma predisposition syndrome	rs587593493, rs527236213, rs527236212

Show/Hide Text Mining Associations (7)

Disease Name	Relationship Type	References
Associations from Text Mining
Carcinogenesis	Inhibit	28053116
Carcinoma Hepatocellular	Associate	28053116, 30893605
Cutis Laxa Autosomal Recessive Type IIB	Associate	28053116
DNA Virus Infections	Associate	27871366, 34879279
Drug Related Side Effects and Adverse Reactions	Associate	27871366
Neoplasms	Associate	27871366, 33558481
Progeria	Associate	30893605

SPRTN (SprT-like N-terminal domain)