NUFIP2

nuclear FMR1 interacting protein 2

Basic information

Region (hg38): 17:29255839-29294148

Links

ENSG00000108256 ∙ NCBI:57532 ∙ OMIM:609356 ∙ HGNC:17634 ∙ Uniprot:Q7Z417 ∙ 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 NUFIP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUFIP2 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				8	2	10
missense			28	5	3	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	28	13	5

Variants in NUFIP2

This is a list of pathogenic ClinVar variants found in the NUFIP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-29286136-C-T		not specified	Uncertain significance (Jan 24, 2024)
17-29286138-T-C		not specified	Uncertain significance (Mar 29, 2023)
17-29286151-G-T		not specified	Uncertain significance (Aug 29, 2022)
17-29286156-A-C		not specified	Uncertain significance (Aug 17, 2022)
17-29286236-A-C		not specified	Uncertain significance (Aug 28, 2021)
17-29286290-C-T			Likely benign (Dec 13, 2017)
17-29286332-T-C			Benign (Oct 23, 2018)
17-29286364-A-G			Likely benign (Jun 13, 2018)
17-29286455-A-G			Likely benign (Jun 14, 2018)
17-29286476-C-T			Likely benign (Apr 17, 2018)
17-29286573-T-C		not specified	Uncertain significance (Apr 08, 2022)
17-29286658-T-C		not specified	Likely benign (Oct 14, 2023)
17-29286658-T-G		not specified	Uncertain significance (Feb 28, 2023)
17-29286675-G-C		not specified	Uncertain significance (Jun 18, 2021)
17-29286678-G-A		not specified	Uncertain significance (May 26, 2024)
17-29286699-C-T		not specified	Uncertain significance (Jul 14, 2022)
17-29286717-T-C		not specified	Likely benign (Mar 20, 2023)
17-29286759-G-A		not specified	Uncertain significance (Jul 06, 2021)
17-29286762-G-T		not specified	Uncertain significance (May 28, 2024)
17-29286820-T-C			Likely benign (Dec 31, 2019)
17-29286879-T-C		not specified	Uncertain significance (Oct 26, 2022)
17-29286886-T-G		not specified	Uncertain significance (Jan 16, 2024)
17-29286989-G-T			Likely benign (Nov 15, 2018)
17-29287018-C-G		not specified	Uncertain significance (Mar 31, 2023)
17-29287045-C-A		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUFIP2	protein_coding	protein_coding	ENST00000225388	4	38283

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00109	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.604	322	354	0.910	0.0000172	4582
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds RNA. {ECO:0000269|PubMed:12837692}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.00703
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.96

Haploinsufficiency Scores

• pHI: 0.465
• hipred: Y
• hipred_score: 0.654
• ghis: 0.504

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.686

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nufip2

Gene ontology

• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;cytoplasmic stress granule;membrane;nuclear body;polysomal ribosome
• Molecular function: RNA binding;protein binding