NIP7

nucleolar pre-rRNA processing protein NIP7, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 16:69337996-69343106

Links

ENSG00000132603 ∙ NCBI:51388 ∙ OMIM:619204 ∙ HGNC:24328 ∙ Uniprot:Q9Y221 ∙ 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 NIP7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIP7 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						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	10	1	1

Variants in NIP7

This is a list of pathogenic ClinVar variants found in the NIP7 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-69339024-T-C			Benign (Sep 05, 2018)
16-69339162-C-T		COG8-congenital disorder of glycosylation	Uncertain significance (Oct 29, 2021)
16-69339166-C-T		COG8-related disorder	Likely benign (Apr 18, 2018)
16-69339196-G-C		COG8-congenital disorder of glycosylation	Likely benign (Oct 13, 2023)
16-69339199-C-T			Likely benign (Jul 06, 2018)
16-69339244-C-G		COG8-congenital disorder of glycosylation	Likely benign (Dec 31, 2019)
16-69339245-A-T		COG8-congenital disorder of glycosylation	Uncertain significance (Jan 15, 2018)
16-69339246-G-A		COG8-congenital disorder of glycosylation	Likely benign (Apr 27, 2018)
16-69339249-G-A		Inborn genetic diseases	Uncertain significance (Apr 04, 2023)
16-69339273-C-T		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
16-69339301-G-A		COG8-congenital disorder of glycosylation	Likely benign (Jul 11, 2022)
16-69339304-G-C		COG8-congenital disorder of glycosylation	Conflicting classifications of pathogenicity (Jul 04, 2021)
16-69339306-C-T		Inborn genetic diseases	Uncertain significance (Feb 12, 2024)
16-69339313-G-A		COG8-congenital disorder of glycosylation	Likely benign (May 21, 2022)
16-69339360-G-T		COG8-congenital disorder of glycosylation	Uncertain significance (Mar 20, 2023)
16-69339361-C-A		COG8-congenital disorder of glycosylation • Inborn genetic diseases	Uncertain significance (Jan 29, 2024)
16-69339386-G-A		Inborn genetic diseases	Uncertain significance (Mar 16, 2022)
16-69339389-C-G		COG8-congenital disorder of glycosylation	Uncertain significance (May 29, 2023)
16-69339391-G-A			Likely benign (Nov 01, 2024)
16-69339401-C-T		Inborn genetic diseases	Uncertain significance (May 05, 2023)
16-69339402-G-A		COG8-congenital disorder of glycosylation	Uncertain significance (Sep 01, 2021)
16-69339402-G-T		not specified	Likely benign (Mar 30, 2016)
16-69339406-G-A		COG8-congenital disorder of glycosylation	Likely benign (Dec 09, 2023)
16-69339407-T-C			Uncertain significance (Jun 01, 2024)
16-69339420-C-G		COG8-congenital disorder of glycosylation	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIP7	protein_coding	protein_coding	ENST00000254940	5	3682

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.364	0.625	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.189	96	101	0.947	0.00000502	1169
Missense in Polyphen		32	29.881	1.0709		393
Synonymous	-1.36	52	41.0	1.27	0.00000207	361
Loss of Function	2.15	2	8.92	0.224	4.42e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000621	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000528	0.0000462
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for proper 34S pre-rRNA processing and 60S ribosome subunit assembly. {ECO:0000269|PubMed:22195017}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.136
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.199
• hipred: Y
• hipred_score: 0.656
• ghis: 0.650

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nip7
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: ribosome assembly;ribosomal large subunit biogenesis
• Cellular component: nucleus;nucleolus;cytosol;preribosome, large subunit precursor
• Molecular function: RNA binding;protein binding