NVL

nuclear VCP like, the group of MicroRNA protein coding host genes|AAA ATPases

Basic information

Region (hg38): 1:224227333-224330189

Links

ENSG00000143748 ∙ NCBI:4931 ∙ OMIM:602426 ∙ HGNC:8070 ∙ Uniprot:O15381 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NVL gene.

• Inborn genetic diseases (16 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NVL gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	2	0

Variants in NVL

This is a list of pathogenic ClinVar variants found in the NVL region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-224227651-C-T		not specified	Uncertain significance (Sep 13, 2023)
1-224227652-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-224233216-T-C		not specified	Uncertain significance (Dec 30, 2023)
1-224233246-C-A		not specified	Uncertain significance (Feb 16, 2023)
1-224268091-T-A		not specified	Uncertain significance (Jan 03, 2024)
1-224275372-C-T			Likely benign (Aug 01, 2022)
1-224281155-T-G		not specified	Uncertain significance (Jan 26, 2022)
1-224287942-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-224287957-G-C		not specified	Uncertain significance (Sep 23, 2023)
1-224289599-T-C		not specified	Likely benign (Feb 05, 2024)
1-224289693-C-T		not specified	Likely benign (Nov 03, 2023)
1-224289698-G-A		not specified	Uncertain significance (Dec 30, 2023)
1-224294303-A-G		not specified	Uncertain significance (Nov 03, 2022)
1-224294309-C-T		not specified	Uncertain significance (Nov 07, 2022)
1-224294347-C-T			Likely benign (Apr 01, 2022)
1-224294355-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-224294385-G-A		not specified	Uncertain significance (Dec 28, 2022)
1-224296576-T-C		not specified	Uncertain significance (Feb 07, 2023)
1-224303839-T-C		not specified	Uncertain significance (Aug 30, 2021)
1-224305156-T-G		not specified	Uncertain significance (Sep 26, 2022)
1-224305166-C-T		not specified	Uncertain significance (Jan 18, 2023)
1-224308091-C-T		not specified	Uncertain significance (Sep 27, 2021)
1-224308172-T-C		not specified	Uncertain significance (Jun 12, 2023)
1-224308226-T-C		not specified	Uncertain significance (Jan 26, 2022)
1-224311818-T-G		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NVL	protein_coding	protein_coding	ENST00000281701	23	103054

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.26e-19	0.656	125636	0	111	125747	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	366	462	0.792	0.0000242	5560
Missense in Polyphen		108	174.09	0.62037		1935
Synonymous	0.394	158	164	0.961	0.00000836	1680
Loss of Function	2.01	37	52.7	0.702	0.00000325	587

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00110
Ashkenazi Jewish	0.000794	0.000794
East Asian	0.000770	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000344	0.000343
Middle Eastern	0.000770	0.000598
South Asian	0.000590	0.000588
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in the assembly of the telomerase holoenzyme and effecting of telomerase activity via its interaction with TERT (PubMed:22226966). Involved in both early and late stages of the pre-rRNA processing pathways (PubMed:26166824). Spatiotemporally regulates 60S ribosomal subunit biogenesis in the nucleolus (PubMed:15469983, PubMed:16782053, PubMed:29107693, PubMed:26456651). Catalyzes the release of specific assembly factors, such as WDR74, from pre-60S ribosomal particles through the ATPase activity (PubMed:29107693, PubMed:26456651, PubMed:28416111). {ECO:0000269|PubMed:15469983, ECO:0000269|PubMed:16782053, ECO:0000269|PubMed:22226966, ECO:0000269|PubMed:26166824, ECO:0000269|PubMed:26456651, ECO:0000269|PubMed:28416111, ECO:0000269|PubMed:29107693}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.127
• rvis_EVS: 0.56
• rvis_percentile_EVS: 81.67

Haploinsufficiency Scores

• pHI: 0.104
• hipred: Y
• hipred_score: 0.590
• ghis: 0.550

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.701

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nvl

Gene ontology

• Biological process: rRNA processing;positive regulation of protein binding;ribosome biogenesis;ribosomal large subunit biogenesis;positive regulation of telomerase activity;regulation of protein localization to nucleolus
• Cellular component: nuclear exosome (RNase complex);nucleus;nucleoplasm;telomerase holoenzyme complex;nucleolus;membrane
• Molecular function: RNA binding;protein binding;ATP binding;ATPase activity;preribosome binding