NVL nuclear VCP like [Homo sapiens (human)] - Gene

Summary

Official Symbol: NVLprovided by HGNC
Official Full Name: nuclear VCP likeprovided by HGNC
Primary source: HGNC:HGNC:8070
See related: Ensembl:ENSG00000143748 MIM:602426; AllianceGenome:HGNC:8070
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NVL2
Summary: This gene encodes a member of the AAA (ATPases associated with diverse cellular activities) superfamily. Multiple transcript variants encoding different isoforms have been found for this gene. Two encoded proteins, described as major and minor isoforms, have been localized to distinct regions of the nucleus. The largest encoded protein (major isoform) has been localized to the nucleolus and shown to participate in ribosome biosynthesis (PMID: 15469983, 16782053), while the minor isoform has been localized to the nucleoplasmin. [provided by RefSeq, Aug 2011]
Expression: Ubiquitous expression in skin (RPKM 7.5), lymph node (RPKM 5.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q42.11

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (224227345..224330172, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (223416266..223519053, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (224415047..224517874, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactome analysis of the Tudor domain-containing protein SPF30 which associates with the MTR4-exosome RNA-decay machinery under the regulation of AAA-ATPase NVL2.
Title: Interactome analysis of the Tudor domain-containing protein SPF30 which associates with the MTR4-exosome RNA-decay machinery under the regulation of AAA-ATPase NVL2.
Data show that the nuclear exosome adaptors nuclear valosin-containing protein-like (NVL) and zinc finger, CCHC domain containing 8 protein (ZCCHC8) bind the Mtr4 exosome RNA helicase (MTR4) KOW domain on a surface.
Title: The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs.
knockdown of WDR74 leads to significant defects in the pre-rRNA cleavage within the internal transcribed spacer 1, occurring in an early stage of the processing pathway. When the dissociation of WDR74 from the MTR4-containing exonuclease complex was impaired upon expression of mutant NVL2, the same processing defect, with partial migration of WDR74 from the nucleolus towards the nucleoplasm, was observed.
Title: WDR74 participates in an early cleavage of the pre-rRNA processing pathway in cooperation with the nucleolar AAA-ATPase NVL2.
Results indicated that the NVL gene may contain overlapping common genetic risk factors for major depressive disorder and schizophrenia in the Han Chinese population
Title: The NVL gene confers risk for both major depressive disorder and schizophrenia in the Han Chinese population.
results suggest that WDR74 is a novel regulatory protein of the MTR4-exsosome complex whose interaction is regulated by NVL2 and is involved in ribosome biogenesis
Title: AAA-ATPase NVL2 acts on MTR4-exosome complex to dissociate the nucleolar protein WDR74.
suggest that NVL2 is involved in pre-rRNA processing by associating with the nuclear exosome complex and that MPP6 is required for maintaining the integrity of this rRNA processing complex
Title: NVL2, a nucleolar AAA-ATPase, is associated with the nuclear exosome and is involved in pre-rRNA processing.
these findings suggest that NVL2 is essential for telomerase biogenesis and provides an alternative approach for inhibiting telomerase activity in cancer.
Title: The AAA-ATPase NVL2 is a telomerase component essential for holoenzyme assembly.
NVL2 might facilitate the dissociation and recycling of nucleolin, thereby promoting efficient ribosome biogenesis
Title: Structure and function of the N-terminal nucleolin binding domain of nuclear valosin-containing protein-like 2 (NVL2) harboring a nucleolar localization signal.
Observational study of gene-disease association. (HuGE Navigator)
Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
interaction of NVL2 with ribosomal protein L5 is ATP-dependent and likely contributes to the nucleolar translocation of NVL2
Title: NVL2 is a nucleolar AAA-ATPase that interacts with ribosomal protein L5 through its nucleolar localization sequence.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of major depressive disorder: new results, meta-analysis, and lessons learned. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-52483 (e-PCR)
- UniSTS:4630

D1S2763 (e-PCR)
- UniSTS:11044

L18426 (e-PCR)
- UniSTS:34648

AFM249yg9 (e-PCR)
- UniSTS:43890

D11S3114 (e-PCR)
- UniSTS:152207

SHGC-84009 (e-PCR)
- UniSTS:104633

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	HDA more info	PubMed
enables preribosome binding	IBA Inferred from Biological aspect of Ancestor more info
enables preribosome binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in positive regulation of protein binding	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of telomerase activity	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of telomerase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rRNA processing	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of protein localization to nucleolus	IDA Inferred from Direct Assay more info	PubMed
involved_in ribosomal large subunit biogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in ribosomal large subunit biogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ribosome biogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in ribosome biogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in membrane	HDA more info	PubMed
part_of nuclear exosome (RNase complex)	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of telomerase holoenzyme complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: nuclear valosin-containing protein-like

Names: NVLp

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029641.1 RefSeqGene

Range

5018..107845

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001243146.2 → NP_001230075.1 nuclear valosin-containing protein-like isoform 3

See identical proteins and their annotated locations for NP_001230075.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks three alternate coding exons in the 5' coding region, uses a downstream initiation codon, and contains an alternate in-frame exon, compared to variant 1. The resulting protein (isoform 3) is shorter and has a distinct N-terminus compared to isoform 1.

Source sequence(s)

AC092809, AK297396, BP284587, BU683548

Consensus CDS

CCDS58062.1

UniProtKB/Swiss-Prot

O15381

Related

ENSP00000341362.4, ENST00000340871.8

Conserved Domains (3) summary

COG0464
Location:68 → 663

SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]

pfam00004
Location:429 → 559

AAA; ATPase family associated with various cellular activities (AAA)

cl21455
Location:409 → 445

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
NM_001243147.2 → NP_001230076.1 nuclear valosin-containing protein-like isoform 4

See identical proteins and their annotated locations for NP_001230076.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AC092809, AK298244, BP284587, BU683548

Consensus CDS

CCDS58063.1

UniProtKB/TrEMBL

B4DLM8

Related

ENSP00000417826.1, ENST00000469075.5

Conserved Domains (5) summary

COG0464
Location:193 → 761

SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]

pfam00004
Location:527 → 657

AAA; ATPase family associated with various cellular activities (AAA)

pfam16725
Location:2 → 72

Nucleolin_bd; Nucleolin binding domain

cl11522
Location:75 → 125

Tom22; Mitochondrial import receptor subunit Tom22

cl21455
Location:507 → 543

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
NM_002533.4 → NP_002524.2 nuclear valosin-containing protein-like isoform 1

See identical proteins and their annotated locations for NP_002524.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1, also known as NVL.2 or the major isoform).

Source sequence(s)

AC092809, AK293923, BP284587, BU683548, U68140

Consensus CDS

CCDS1541.1

UniProtKB/Swiss-Prot

B4DMC4, B4DP98, O15381, Q96EM7

UniProtKB/TrEMBL

B4DLM8

Related

ENSP00000281701.6, ENST00000281701.11

Conserved Domains (4) summary

COG0464
Location:284 → 852

SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]

pfam00004
Location:618 → 748

AAA; ATPase family associated with various cellular activities (AAA)

pfam16725
Location:2 → 72

Nucleolin_bd; Nucleolin binding domain

cl21455
Location:598 → 634

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
NM_206840.3 → NP_996671.1 nuclear valosin-containing protein-like isoform 2

See identical proteins and their annotated locations for NP_996671.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate exon and uses a downstream start codon compared to variant 1. The resulting protein (isoform 2, also known as NVL.1 or the minor isoform) is shorter and has a distinct N-terminus compared to isoform 1.

Source sequence(s)

AC092809, AK293923, BP284587, BU683548, U78772

Consensus CDS

CCDS1542.1

UniProtKB/TrEMBL

B4DLM8

Related

ENSP00000375747.2, ENST00000391875.6

Conserved Domains (1) summary

cl27568
Location:137 → 750

TIP49; TIP49 C-terminus

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

224227345..224330172 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017001383.2 → XP_016856872.1 nuclear valosin-containing protein-like isoform X5

UniProtKB/TrEMBL

B4DLM8
XM_011544196.1 → XP_011542498.1 nuclear valosin-containing protein-like isoform X4

UniProtKB/TrEMBL

B4DLM8

Conserved Domains (4) summary

COG0464
Location:284 → 879

SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]

pfam00004
Location:645 → 775

AAA; ATPase family associated with various cellular activities (AAA)

pfam16725
Location:2 → 72

Nucleolin_bd; Nucleolin binding domain

cl21455
Location:625 → 661

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
XM_017001379.2 → XP_016856868.1 nuclear valosin-containing protein-like isoform X2

UniProtKB/TrEMBL

B4DLM8
XM_017001378.2 → XP_016856867.1 nuclear valosin-containing protein-like isoform X1

UniProtKB/TrEMBL

B4DLM8
XM_047421613.1 → XP_047277569.1 nuclear valosin-containing protein-like isoform X7
XM_017001380.3 → XP_016856869.1 nuclear valosin-containing protein-like isoform X3

UniProtKB/TrEMBL

B4DLM8
XM_047421631.1 → XP_047277587.1 nuclear valosin-containing protein-like isoform X12
XM_047421621.1 → XP_047277577.1 nuclear valosin-containing protein-like isoform X10
XM_047421618.1 → XP_047277574.1 nuclear valosin-containing protein-like isoform X8
XM_017001384.2 → XP_016856873.1 nuclear valosin-containing protein-like isoform X6

UniProtKB/TrEMBL

B4DLM8
XM_047421637.1 → XP_047277593.1 nuclear valosin-containing protein-like isoform X14
XM_047421635.1 → XP_047277591.1 nuclear valosin-containing protein-like isoform X13
XM_047421626.1 → XP_047277582.1 nuclear valosin-containing protein-like isoform X11
XM_017001385.3 → XP_016856874.1 nuclear valosin-containing protein-like isoform X9

UniProtKB/TrEMBL

B4DLM8

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

223416266..223519053 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054336810.1 → XP_054192785.1 nuclear valosin-containing protein-like isoform X5
XM_054336809.1 → XP_054192784.1 nuclear valosin-containing protein-like isoform X4
XM_054336807.1 → XP_054192782.1 nuclear valosin-containing protein-like isoform X2
XM_054336806.1 → XP_054192781.1 nuclear valosin-containing protein-like isoform X1
XM_054336812.1 → XP_054192787.1 nuclear valosin-containing protein-like isoform X7
XM_054336808.1 → XP_054192783.1 nuclear valosin-containing protein-like isoform X3
XM_054336817.1 → XP_054192792.1 nuclear valosin-containing protein-like isoform X12
XM_054336815.1 → XP_054192790.1 nuclear valosin-containing protein-like isoform X10
XM_054336813.1 → XP_054192788.1 nuclear valosin-containing protein-like isoform X8
XM_054336811.1 → XP_054192786.1 nuclear valosin-containing protein-like isoform X6
XM_054336819.1 → XP_054192794.1 nuclear valosin-containing protein-like isoform X14
XM_054336818.1 → XP_054192793.1 nuclear valosin-containing protein-like isoform X13
XM_054336816.1 → XP_054192791.1 nuclear valosin-containing protein-like isoform X11
XM_054336814.1 → XP_054192789.1 nuclear valosin-containing protein-like isoform X9