NIP7

protein-coding

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

Gene summary

Enables RNA binding activity. Predicted to be involved in ribosomal large subunit biogenesis. Located in nucleolus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_016101.5

Inheritance

—

ClinVar variants

U:30B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr16:69,337,996-69,343,106

External References & Databases

Ensembl (ENSG00000132603)

Transcript & Mutation Effects

hg38 • Region Span ~5.1 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NIP7 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 29

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016101.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			29 clinvar	1 clinvar		30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	1	0	31

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016101.5	RefSeq	NP_057185.1	5	MANE Select
ENST00000254940.10	Ensembl	ENSP00000254940.5	5	MANE Select
NM_001199434.2	RefSeq	NP_001186363.1	4	Standard
ENST00000254941.6	Ensembl	ENSP00000254941.6	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

ribosome assembly
ribosomal large subunit biogenesis

Molecular Function

RNA binding
protein binding

Cellular Component

nucleus
nucleolus
cytosol
preribosome, large subunit precursor

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000254940
Coding exons: 5
Length: 3682
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125748
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.189	96	101	0.947	0.00000502	1169
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000053	0.000046	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.824

Gene Damage Prediction

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