NUFIP2

protein-coding

nuclear FMR1 interacting protein 2

Gene summary

Enables RNA binding activity. Located in several cellular components, including cytoplasmic stress granule; nuclear body; and ribosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020772.3

Inheritance

—

ClinVar variants

U:100B:21

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr17:29,255,839-29,294,148

External References & Databases

Ensembl (ENSG00000108256)

Transcript & Mutation Effects

hg38 • Region Span ~38.3 kb

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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 NUFIP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 98

not providedTotal: 18

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020772.3. 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				8 clinvar	2 clinvar	10
missense			97 clinvar	8 clinvar	3 clinvar	108
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	100	16	5	121

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020772.3	RefSeq	NP_065823.1	4	MANE Select
ENST00000225388.9	Ensembl	ENSP00000225388.3	4	MANE Select
ENST00000579665.1	Ensembl	ENSP00000463450.1	3	Standard
ENST00000579665.2	Ensembl	ENSP00000463450.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in epithelium - TarBase
miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase

Molecular Function

RNA binding
protein binding

Cellular Component

nucleus
nucleoplasm
cytoplasm
cytosol
cytoplasmic stress granule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000225388
Coding exons: 4
Length: 38283
Individuals with no LoFs: 125744
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125748
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.604	322	354	0.910	0.0000172	4582
Missense (PolyPhen)		71	102.63	0.69183		1345
Synonymous	-2.03	163	133	1.22	0.00000671	1348
Loss of Function	4.37	1	24.2	0.0413	0.00000120	318

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds RNA. {ECO:0000269|PubMed:12837692}.;

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.00703
RVIS EVS: 0.53
RVIS percentile EVS: 80.96

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.686

Gene Damage Prediction

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