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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	79650
Gene name	U6 snRNA biogenesis phosphodiesterase 1
Gene symbol	USB1
Synonyms (NCBI Gene)	C16orf57HVSL1Mpn1PNhMpn1hUsb1
Chromosome	16
Chromosome location	16q21
Summary	This gene encodes a protein with several conserved domains, however, its exact function is not known. Mutations in this gene are associated with poikiloderma with neutropenia (PN), which shows phenotypic overlap with Rothmund-Thomson syndrome (RTS) caused

Show/Hide all (19)

SNP ID	Visualize variation	Clinical significance	Consequence
rs137853970	A>C	Pathogenic	Genic downstream transcript variant, splice acceptor variant
rs137853971	A>G	Pathogenic	Intron variant, coding sequence variant, genic downstream transcript variant, missense variant
rs137853972	AGGAACTACAGG>-	Pathogenic	Genic downstream transcript variant, coding sequence variant, splice donor variant
rs771096742	T>A,C	Pathogenic	Coding sequence variant, stop gained, synonymous variant
rs777667891	TCAA>-	Pathogenic	Genic downstream transcript variant, frameshift variant, intron variant, coding sequence variant
rs1249059283	A>C,G	Pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant
rs1292827495	G>T	Pathogenic	Splice donor variant, genic downstream transcript variant
rs1459714680	C>T	Pathogenic	Genic downstream transcript variant, coding sequence variant, stop gained
rs1555498092	G>A	Pathogenic	Splice acceptor variant
rs1555498117	->C	Pathogenic	Frameshift variant, coding sequence variant
rs1555498120	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1555498129	C>T	Pathogenic	Stop gained, coding sequence variant
rs1555498396	A>G	Pathogenic	Intron variant, genic downstream transcript variant, splice acceptor variant
rs1555498399	A>-	Pathogenic	Frameshift variant, intron variant, genic downstream transcript variant, coding sequence variant
rs1555498563	T>G	Pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant
rs1555498565	A>-	Pathogenic	Frameshift variant, genic downstream transcript variant, coding sequence variant
rs1555498573	C>T	Pathogenic	Stop gained, genic downstream transcript variant, coding sequence variant
rs1555498581	G>A	Pathogenic	Splice donor variant, genic downstream transcript variant
rs1597049287	T>C	Likely-pathogenic	Coding sequence variant, missense variant

Show/Hide all (36)

miRTarBase ID	miRNA	Experiments	Reference
MIRT028794	hsa-miR-26b-5p	Microarray	19088304
MIRT050173	hsa-miR-26a-5p	CLASH	23622248
MIRT491593	hsa-miR-4524b-3p	PAR-CLIP	23592263
MIRT491591	hsa-miR-6758-5p	PAR-CLIP	23592263
MIRT491592	hsa-miR-6856-5p	PAR-CLIP	23592263
MIRT491590	hsa-miR-3125	PAR-CLIP	23592263
MIRT491589	hsa-miR-3916	PAR-CLIP	23592263
MIRT491588	hsa-miR-6859-5p	PAR-CLIP	23592263
MIRT491587	hsa-miR-4779	PAR-CLIP	23592263
MIRT491586	hsa-miR-4524a-3p	PAR-CLIP	23592263
MIRT491585	hsa-miR-3150b-3p	PAR-CLIP	23592263
MIRT491584	hsa-miR-4784	PAR-CLIP	23592263
MIRT491583	hsa-miR-6077	PAR-CLIP	23592263
MIRT491582	hsa-miR-185-5p	PAR-CLIP	23592263
MIRT491581	hsa-miR-4306	PAR-CLIP	23592263
MIRT491580	hsa-miR-4644	PAR-CLIP	23592263
MIRT491579	hsa-miR-765	PAR-CLIP	23592263
MIRT491577	hsa-miR-7106-5p	PAR-CLIP	23592263
MIRT491578	hsa-miR-6825-5p	PAR-CLIP	23592263
MIRT491593	hsa-miR-4524b-3p	PAR-CLIP	23592263
MIRT491591	hsa-miR-6758-5p	PAR-CLIP	23592263
MIRT491592	hsa-miR-6856-5p	PAR-CLIP	23592263
MIRT491590	hsa-miR-3125	PAR-CLIP	23592263
MIRT491589	hsa-miR-3916	PAR-CLIP	23592263
MIRT491588	hsa-miR-6859-5p	PAR-CLIP	23592263
MIRT491587	hsa-miR-4779	PAR-CLIP	23592263
MIRT491586	hsa-miR-4524a-3p	PAR-CLIP	23592263
MIRT491585	hsa-miR-3150b-3p	PAR-CLIP	23592263
MIRT491584	hsa-miR-4784	PAR-CLIP	23592263
MIRT491583	hsa-miR-6077	PAR-CLIP	23592263
MIRT491582	hsa-miR-185-5p	PAR-CLIP	23592263
MIRT491581	hsa-miR-4306	PAR-CLIP	23592263
MIRT491580	hsa-miR-4644	PAR-CLIP	23592263
MIRT491579	hsa-miR-765	PAR-CLIP	23592263
MIRT491577	hsa-miR-7106-5p	PAR-CLIP	23592263
MIRT491578	hsa-miR-6825-5p	PAR-CLIP	23592263

Show/Hide all (20)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000175	Function	3'-5'-RNA exonuclease activity	IBA
GO:0000175	Function	3'-5'-RNA exonuclease activity	IDA	23190533, 30215753
GO:0000175	Function	3'-5'-RNA exonuclease activity	IEA
GO:0004518	Function	Nuclease activity	IEA
GO:0005515	Function	Protein binding	IPI	23022480
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	22899009, 23022480
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0008380	Process	RNA splicing	IMP	22899009
GO:0016787	Function	Hydrolase activity	IEA
GO:0016829	Function	Lyase activity	IEA
GO:0034472	Process	SnRNA 3'-end processing	IMP	26213367
GO:0034477	Process	U6 snRNA 3'-end processing	IBA
GO:0034477	Process	U6 snRNA 3'-end processing	IDA	23190533
GO:0034477	Process	U6 snRNA 3'-end processing	IEA
GO:0034477	Process	U6 snRNA 3'-end processing	IMP	22899009, 23022480, 26213367
GO:0045171	Component	Intercellular bridge	IDA
GO:1990838	Function	Poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends	IDA	23022480, 23190533, 26213367, 28887445, 31832688
GO:1990838	Function	Poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends	IEA

MIM	HGNC	e!Ensembl
613276	25792	ENSG00000103005

Q9BQ65

Protein name

U6 snRNA phosphodiesterase 1 (hUsb1) (3'-5' RNA exonuclease USB1) (EC 4.6.1.-) (Mutated in poikiloderma with neutropenia protein 1) (Mutated in PN protein 1) (hMpn1)

Protein function

3'-5' RNA exonuclease that trims the 3' end of oligo(U) and oligo(A) tracts of the pre-U6 small nuclear RNA (snRNA) molecule, leading to the formation of a mature U6 snRNA 3' end-terminated with a 2',3'-cyclic phosphate (PubMed:22899009, PubMed:

PDB

4H7W , 5V1M , 6D2Z , 6D30 , 6D31

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF09749	HVSL	43 → 263	Uncharacterised conserved protein	Family

Sequence

MSAAPLVGYSSSGSEDESEDGMRTRPGDGSHRRGQSPLPRQRFPVPDSVLNMFPGTEEGP
EDDSTKHGGRVRTFPHERGNWATHVYVPYEAKEEFLDLLDVLLPHAQTYVPRLVRMKVFH
LSLSQSVVLRHHWILPFVQALKARMTSFHRFFFTANQVKIYTNQEKTRTFIGLEVTSGHA
QFLDLVSEVDRVMEEFNLTTFYQDPSFHLSLAWCVGDARLQLEGQCLQELQAIVDGFEDA
EVLLRVHTEQVRCKSGNKFFSMPLK

Sequence length

265

Interactions

View interactions

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Poikiloderma with neutropenia	Likely pathogenic; Pathogenic	rs747958554, rs137853970, rs137853972, rs137853971, rs137853973, rs786205051, rs1555498399, rs1555498565, rs1555498573, rs1249059283, rs1459714680, rs1292827495, rs759761915, rs1555498092, rs1555498129 View all (3 more)	RCV002504642 RCV000000224 RCV000000225 RCV000000226 RCV000144431 RCV000000227 RCV000598668 RCV000598696 RCV000599164 RCV000599396 RCV000598691 RCV000599560 RCV000598852 RCV000599282 RCV000599306 RCV000598593 RCV000677661 RCV000985173
USB1-related disorder	Likely pathogenic; Pathogenic	rs747958554	RCV004758163

Show/Hide Unknown Diseases (10)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign	rs16959640	RCV005914182
Cervical cancer	Benign	rs16959640, rs9924482	RCV005914184 RCV005918061
Cholangiocarcinoma	Benign	rs16959640	RCV005914189
Gastric cancer	Benign	rs16959640	RCV005914186
Lung cancer	Benign	rs16959640, rs9924482	RCV005914190 RCV005918064
Malignant lymphoma, large B-cell, diffuse	Benign	rs9924482	RCV005918062
Malignant tumor of esophagus	Benign	rs16959640	RCV005914183
Ovarian serous cystadenocarcinoma	Benign	rs16959640	RCV005914187
Sarcoma	Benign	rs16959640, rs9924482	RCV005914185 RCV005918063
Uterine carcinosarcoma	Benign	rs16959640	RCV005914188

Show/Hide Text Mining Associations (24)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Abnormalities Drug Induced	Associate	31522452
Breast Neoplasms	Associate	26872609
Carcinogenesis	Associate	26872609
Cholangiocarcinoma	Associate	32020235
Dubowitz syndrome	Associate	27612988
Dyskeratosis Congenita	Associate	20817924, 22899009, 27612988
Dystonic Disorders	Associate	26306619
Ectodermal Dysplasia	Associate	27612988
Ectrodactyly	Associate	26546903
Genetic Diseases Inborn	Associate	23190533
Growth Disorders	Associate	27612988
Leukemia Myeloid Acute	Associate	37164308
Lung Diseases	Associate	26273833
Myelodysplastic Syndromes	Associate	26306619
Neoplasms	Inhibit	24887023
Neoplasms	Associate	26306619, 26872609, 27028305
Neural Tube Defects	Associate	26306619
Neutropenia	Associate	20817924, 22899009, 26213367, 26987923, 27612988, 35522049
Osteosarcoma	Associate	27028305
Pneumonia	Associate	36217141
Poikiloderma with Neutropenia	Associate	20004881, 20817924, 21271650, 22269211, 22899009, 23022480, 23190533, 26213367, 26306619, 26546903, 26987923, 30215753, 31522452
Rett Syndrome	Associate	20817924
Rothmund Thomson Syndrome	Associate	20004881, 20817924, 22899009, 26213367, 27612988, 35522049
Stomach Neoplasms	Inhibit	24887023

USB1 (U6 snRNA biogenesis phosphodiesterase 1)